Professional Documents
Culture Documents
REVIEWS
Intestinal epithelial cells: regulators
of barrier function and immune
homeostasis
Lance W.Peterson1 and David Artis1,2
Abstract | The abundance of innate and adaptive immune cells that reside together with
trillions of beneficial commensal microorganisms in the mammalian gastrointestinal
tract requires barrier and regulatory mechanisms that conserve hostmicrobial
interactions and tissue homeostasis. This homeostasis depends on the diverse functions
of intestinal epithelial cells (IECs), which include the physical segregation of commensal
bacteria and the integration of microbial signals. Hence, IECs are crucial mediators of
intestinal homeostasis that enable the establishment of an immunological environment
permissive to colonization by commensal bacteria. In this Review, we provide a
comprehensive overview of how IECs maintain hostcommensal microbial relationships
and immune cell homeostasis in the intestine.
Mucins
Heavily glycosylated proteins
that are the major component
of the mucus that coats
epithelial barrier surfaces.
Department of Microbiology
and Institute for Immunology,
Perelman School of Medicine,
University of Pennsylvania.
2
Department of Pathobiology,
School of Veterinary
Medicine, University of
Pennsylvania, Philadelphia,
Pennsylvania 19104, USA.
emails: lancep@mail.med.
upenn.edu;
dartis@mail.med.upenn.edu
doi:10.1038/nri3608
1
R E V IE W S
Small intestine
Follicle-associated epithelium
Colon
Apoptotic
IECs
Commensal
bacteria
Mucus
Secondlayer
mucus
TFF3
sIgA
AMPs
M cell
Mucus
Enteroendocrine
cell
Goblet
cell
Enterocyte
B cell
Stromal
cell
Lymphoid
follicle
Paneth
cell
IESC
Crypts
Tubular invaginations of the
intestinal epithelium. Lining
the base of the crypts are
small intestinal Paneth cells,
which produce numerous
antimicrobial proteins, and
stem cells, which continuously
divide to give rise to the entire
intestinal epithelium.
Villi
Projections of the intestinal
epithelium into the lumen
ofthe small intestine that
havean outer layer
consistingof mature,
absorptive enterocytes,
mucus-secreting goblet cells
and enteroendocrine cells.
Pluripotent intestinal
epithelial stem cells
(Pluripotent IESCs).
Tissue-resident stem cells
thatundergo continuous
self-renewal and are
responsible for regenerating
all lineages of mature
intestinal epithelial cells,
including enterocytes,
enteroendocrine cells,
gobletcells and Paneth cells.
Macrophage
DC
Figure 1 | The IEC barrier. Intestinal epithelial cells (IECs) form a biochemical and physical barrier that maintains
segregation between luminal microbial communities and the mucosal immune system. The
intestinal
epithelial
stem
Nature
Reviews
| Immunology
cell (IESC) niche, containing epithelial, stromal and haematopoietic cells, controls the continuous renewal of the
epithelial cell layer by crypt-resident stem cells. Differentiated IECs with the exception of Paneth cells migrate
up the cryptvillus axis, as indicated by the dashed arrows. Secretory goblet cells and Paneth cells secrete mucus and
antimicrobial proteins (AMPs) to promote the exclusion of bacteria from the epithelial surface. The transcytosis and
luminal release of secretory IgA (sIgA) further contribute to this barrier function. Microfold cells (Mcells) and goblet
cells mediate transport of luminal antigens and live bacteria across the epithelial barrier to dendritic cells (DCs),
and intestine-resident macrophages sample the lumen through transepithelial dendrites. TFF3, trefoil factor 3.
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N H o m e os tat i c I m m un e R e sRpEons
eS
s
V IE W
Box 1 | The IESC niche
Along the cryptvillus axis of the epithelium, pluripotent intestinal epithelial
stem cells (IESCs) residing in the base of crypts give rise to a transit-amplifying
population of cells that undergo rapid proliferation and differentiation into the
various intestinal epithelial cell (IEC) subsets. Terminally differentiated cells with
the exception of Paneth cells migrate up the cryptvillus axis until they are lost
from the epithelial layer. For this process to be maintained, epithelial stem cells
must be able to undergo repeated rounds of replication and possess the capacity
for continuous self-renewal16. Recent advances in stem cell biology have identified
markers of IESCs that have contributed to the understanding of epithelial
self-renewal and differentiation16,183185.
The patterning and distribution of proliferating crypt units in the intestine depend
on paracrine signalling between the epithelium and the underlying mesenchyme.
A balance between bone morphogenetic protein signals and antagonists, such as
noggin and gremlin, provides a niche for proliferating stem cells while limiting ectopic
crypt formation15. IESCs further rely on signalling through both the WNTcatenin
and the Notch pathways for promoting self-renewal and directing differentiation
towards secretory versus non-secretory lineage IEC fates16.
The responsiveness of epithelial progenitors to external regulation in settings of
inflammation or infection remains less well understood. In particular, how immune
system-mediated signalling integrates into the homeostatic pathways described
above or acts through alternative pathways for altering stem cell function is poorly
defined. However, several recent studies have given insight into the regulation of
WNTcatenin signalling by the pro-inflammatory cytokines interferon and tumour
necrosis factor, offering an example of how immune signalling and homeostatic
pathways for regulating the stem cell niche can converge186,187. Furthermore,
cell-intrinsic mechanisms of integrating hostcommensal microorganism interactions
into IEC homeostasis have been recently described188.
Autophagy
A cellular process by which
cytoplasmic organelles and
macromolecular complexes
are engulfed by double
membrane-bound vesicles
for delivery to lysosomes
and subsequent degradation.
This process is involved in
constitutive turnover of
proteins and organelles and is
central to cellular activities that
maintain a balance between
the synthesis and breakdown
of various proteins.
Plasma cells
Terminally differentiated cells
of the Bcell lineage that
secrete large amounts of
antibodies.
Lamina propria
Connective tissue that
underlies the epithelium of the
mucosa and contains stromal
and haematopoietic cells.
R E V IE W S
Box 2 |IEC tight junctions and turnover
Below the mucous layers, intestinal epithelial cells (IECs) form a continuous physical
barrier. Tight junctions connect adjacent IECs and are associated with cytoplasmic
actin and myosin networks that regulate intestinal permeability. In the setting of
inflammatory bowel disease (IBD), dysregulation of these interactions, mediated by
tumour necrosis factor signalling and by myosin light chain kinase activity, leads
to IEC cytoskeletal rearrangements that disrupt tight junctions and increase
permeability189,190. These findings suggest that IEC tight junctions could be important
targets for enhancing the integrity of the intestinal barrier in IBD.
As the IEC barrier is continuously renewed, the turnover of IECs provides an additional
challenge to the maintenance of epithelial continuity. Recent studies have described
pathways by which adjacent cells seal potential voids created during the extrusion of
either apoptotic or live cells from the single-cell layer191,192. As dysregulated epithelial
cell turnover and apoptosis are associated with intestinal inflammation, the contribution
of these mechanisms to the limiting of barrier breaches and further inflammation is of
relevance to our understanding of epithelial cells as an efficient physical barrier.
Although increased intestinal permeability has been correlated with IBD1,193,194,
it remains unclear whether the loss of barrier function is a cause or a consequence of
intestinal inflammation in human disease. Evidence from mouse models with genetic
defects in tight-junction-associated proteins suggests that disruption of barrier
function alone is not always sufficient to cause disease195,196. Notably, in mice with a
deletion of the tight-junction protein junctional adhesion moleculeA, the secretion
of commensal bacteria-specific IgA can compensate for the loss of barrier function
and limit disease severity following chemically induced colitis195. Thus, compensatory
immune mechanisms can act to protect against the development of colitis, even in the
setting of barrier disruption, supporting a multi-hit model of disease susceptibility195.
Peyers patches
Groups of lymphoid aggregates
located in the submucosa of
the small intestine that contain
many immune cells, including
Bcells, Tcells and dendritic
cells. They have a luminal
barrier consisting of specialized
epithelial cells, called microfold
cells, which sample the lumen
and transport antigens.
Pattern-recognition
receptors
(PRRs). Receptors that
recognize structures shared
by foreign microorganisms
or endogenous molecules
associated with pathogenesis.
Signalling through these
receptors promotes
tissue-specific innate immune
responses including the
production of cytokines.
Toll-like receptor
(TLR). An evolutionarily
conserved pattern-recognition
receptor located at the cell
surface or at intracellular
membranes. The natural
ligands of TLRs are conserved
molecular structures found in
bacteria, viruses and fungi.
Sampling of luminal contents by IECs. Despite the barrier function supported by IECs (BOX 2), the intestinal
epithelium includes specialized adaptations that conflict
with the concept of complete segregation between host
immune cells and microorganisms. Specialized IECs,
called microfold cells (Mcells), mediate the sampling
of luminal antigens and intact microorganisms for presentation to the underlying mucosal immune system44.
These specialized IECs are concentrated in the follicleassociated epithelium overlaying the luminal surface of
intestinal lymphoid structures, including Peyers patches
and isolated lymphoid follicles44,45.
Although nonspecific uptake and transcytosis of antigens represents a well-established mechanism of sampling
by Mcells, it has recently been demonstrated that more
efficient mechanisms of receptor-mediated transport also
exist. The surface glycoprotein GP2 acts as a receptor for
the bacterial pilus protein FimH, and the Mcell-mediated
transport of the pathogen Salmonella enterica across the
epithelial barrier depends on GP2FimH interaction46.
This suggests that Mcells are capable of both specific
receptor-mediated microbial uptake and nonspecific
antigen uptake from the intestinal lumen. Although the
active transport of luminal contents across the epithelial
barrier was thought to be a unique function of Mcells, it
was recently shown that small-intestinal goblet cells also
contribute to this process through the delivery of soluble
luminal antigens to subepithelial dendritic cells (DCs)47.
Although both Mcells and goblet cells seem to be capable
of antigen delivery to the lamina propria, the functional
importance and contribution of these two pathways to
the development of anti-pathogen responses or to the
maintenance of immune tolerance remains incompletely
understood.
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N H o m e os tat i c I m m un e R e sRpEons
eS
s
V IE W
a
Commensal bacteria
Mucin
AMPs
TFF3
TLR9
(apical)
ROS
Tight
junction
TLR3,
TLR7,
TLR8
Endosome
MYD88
Ub
Ub
Ub
I B
NLRP3,
NLRP6,
NLRC4
Heat-shock
proteins
IB
p50 p65
NF-B
NF-B
p50 p65
p50 p65
NOD1,
NOD2
Inammasome
RIP2
FRMPD2
IL-1
and IL-18
(NLR). A pattern-recognition
receptor located in the cytosol.
NLRs recognize a wide range of
foreign structures and patterns
associated with pathogenesis.
Some members of this family
form multiprotein complexes
known as inflammasomes,
which regulate the processing
and secretion of
pro-inflammatory cytokines.
RIGIlike receptor
(RLR). A pattern-recognition
receptor located in the cytosol
that responds to viral RNA.
IKK
IKK IKK
NF-B
Pro-caspase 1
NOD-like receptor
TRIF
TLR2, TLR4,
TLR5 or TLR9
EGFR
EGFR ligands
Figure 2 | Microbial recognition promotes IEC health and function. a|Pattern-recognition receptors (PRRs),
including intestinal epithelial cell (IEC)-expressed Toll-like receptors (TLRs) and NOD-like receptors (NLRs), recognize
Nature
| Immunology
conserved microbial-associated molecular motifs and pathogen-specific virulence properties.
TLRsReviews
recruit the
signalling
adaptors MYD88 and TIR-domain-containing adaptor protein inducing interferon (TRIF) on ligation to signal molecules
via nuclear factorB (NFB), p50 and p65 subunit activation and the mitogen-activated protein kinase (MAPK) pathway
(not shown). Nucleotide-binding oligomerization domain 1 (NOD1) and NOD2 signal through receptor-interacting
protein 2 (RIP2) to activate NFB and MAPKs, whereas other IEC-expressed NLRs, including NOD-, LRR- and pyrin
domain-containing3 (NLRP3), NLRP6 and NOD-, LRR- and CARD-containing4 (NLRC4), form inflammasome complexes
with pro-caspase1 for the cleavage and activation of interleukin1 (IL1) and IL18. Polarized expression of PRRs by IECs
at either the apical or basolateral membrane may contribute to the discrimination between commensal and pathogen
microbial signals. For example, signalling through surface or endosomal TLR9 at the apical pole of IECs promotes the
inhibition of NF-B signalling, whereas TLR signalling from the basolateral pole promotes NF-B activation. b|Microbial
recognition is integrated by IECs. This promotes cell survival and repair (mediated by trefoil factor 3 (TFF3), heat-shock
proteins and epidermal growth factor receptor (EGFR) ligand expression), barrier function (mediated by increased mucin
and antimicrobial peptide (AMP) producton) and immunoregulatory responses (mediated by a proliferation-inducing
ligand (APRIL), B cell-activating factor (BAFF), IL-25, retinoic acid, transforming growth factor (TGF) and thymic
stromal lymphopoietin (TSLP)), FRMPD2, FERM and PDZ domain-containing 2; IB, inhibitor of NFB; IKK, IB kinase;
ROS, reactive oxygen species; Ub, ubiquitin.
(IB) kinase (IKK) complex or NFB essential modulator (NEMO), results in enhanced DSS-induced or spontaneous colitis60,61. These studies establish an essential
role for TLRs, in addition to other NFB signalling
pathways, in epithelial homeostasis andrepair.
R E V IE W S
Nuclear factor-B
(NFB). A family of
transcription factors important
for pro-inflammatory and
anti-apoptotic responses that
are activated by the ubiquitindependent degradation of
their respective inhibitors,
members of the inhibitor of
NFB (IB) family. This process
is mediated by the kinases, IB
kinase1 (IKK1) and IKK2.
Inflammasomes
Multiprotein complexes that
contain a member of the
NOD-like receptor family,
adaptor proteins and the
protease caspase 1. These
complexes regulate the
catalytic processing and
secretion of pro-inflammatory
cytokines, including
interleukin1 (IL1) and
IL18.
delicate nature of the balance that exists between homeostasis and inflammation and its importance in maintaining healthy hostmicroorganism symbiosis.
Specialized regulation of PRR pathways in IECs. The
proximity of IECs to an abundance of luminal microbial
signals necessitates specialized mechanisms for maintaining altered or hyporesponsive PRR signalling in response
to commensal bacteria-dependent stimuli83,84. In support
of this, IECs express negative regulators of PRR-dependent
pro-inflammatory signalling 75,83,85,86 (see Supplementary
informationS1 (table)). The disruption of these regulatory pathways or constitutive activation of NFB predispose mice to dysregulated epithelial homeostasis and
exaggerated inflammation72,75,85,87. Furthermore, it has
been appreciated that commensal bacteria-dependent
production of ROS by IECs can attenuate the activation
of NFB, broadly tolerizing IECs to microbial stimulation through PRR signalling 88,89. Although additional
mechanisms exist for the negative regulation of PRR signalling pathways90, in most cases the extent to which they
are active in IECs and their contributions to intestinal
homeostasis remain to be determined.
In addition to maintaining the hyporesponsiveness
of IECs, innate immune pathways must differentiate
between signals derived from commensal and pathogenic microorganisms for the scaling of an appropriate
inflammatory response91. The polarized nature of the
intestinal epithelium allows for the anatomical segregation of PRRs (FIG.2). Invitro and invivo models demonstrate differential responsiveness of IECs to apical versus
basolateral stimulation with multiple TLR ligands9294.
For example, although basolateral exposure of IECs to
TLR9 ligands results in canonical activation and nuclear
translocation of NFB, apical exposure results in a
net inhibitory effect through the stabilization of IB94.
This apical signal induces tolerance to subsequent TLR
stimulation, demonstrating a unique adaptation for the
cross-tolerance of microbial recognition pathways and
a differential response to microbial signals based on
anatomical location94 (FIG.2).
This concept of subcellular segregation and polarized
distribution of TLRs has been translated to the regulation of additional PRR pathways95,96. Through a series
of elegant genetic screens, FERM and PDZ domaincontaining2 (FRMPD2) which is a positive regulator of NOD2mediated NFB activation in response to
MDP recognition was recently identified to act as a
scaffold protein that promotes basolateral membrane
localization and selective basolateral activation through
interactions with the leucine-rich repeat (LRR) domain
of NOD2 (REF. 96) (FIG.2). Common Crohns diseaseassociated variants of NOD2 contain mutations in this
LRR domain. These NOD2-mutant proteins were shown
invitro to lack the ability to interact with FRMPD2, to
colocalize at the basolateral membrane of epithelial cells
and to respond to stimulation with NOD2 ligands62,63,96.
These studies give insight into the mechanism of NOD2
dysfunction associated with IBD and how IECs may
spatially regulate the activation of PRR signals at the
intestinal barrier.
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N H o m e os tat i c I m m un e R e sRpEons
eS
s
V IE W
Finally, mechanisms by which IECs may break their
relative tolerance to microbial signals in settings of pathogen infection are poorly defined. In contrast to sterile
sites in the body, control of inflammation in the intestine may be more adapted to relying on the recognition
of danger signals associated with pathogenesis, rather
than on the presence of microbial signals alone97. The
recognition of danger has been proposed to be mediated through the detection of properties associated with
microbial viability, termed viability-associated PAMPs
(vita-PAMPs), that distinguish living pathogens from
inert microbial debris, as well as through the detection
of conserved virulence factors of pathogens, such as bacterial secretion systems and toxins that penetrate into the
cellular cytosol91,98. Although these mechanisms for scaling microbial threats have been studied and identified in
phagocytes and antigen-presenting cells, their function
and relevance in IECs are less well understood.
Commensal microorganism-dependent regulation of
barrier function. In addition to the homeostatic role of
microbial recognition by IECs, the intestinal epithelium
acts as an essential integrator of environmental signals for
the regulation of microbial colonization, barrier function
and mucosal immune responses. As previously discussed,
the production of an apical mucous layer, the secretion
of broadly targeted AMPs and the transcytosis of secretory IgA contribute to epithelial barrier function. Reduced
mucous layer thickness in germ-free mice can be reversed
by treatment with TLR ligands, indicating that commensal bacteria-dependent signals regulate mucus production by goblet cells17. Similarly, the expression of many
epithelial cell-derived AMPs is enhanced by, or dependent
on, the presence of commensal microbial signals18,29,99101.
As cells with specialized antimicrobial function, Paneth
cells play a particularly important part in the regulation
of AMP production through cell-intrinsic expression of
MYD88 and NOD2 (REFS100,101).
The transport of IgA across the epithelial barrier
is regulated, in part, by the expression of pIgR on the
basolateral membrane of IECs, which is promoted by
MYD88- and NFBdependent signalling in response
to commensal microbial signals40,102. Finally, the integrity of tight junctions and transepithelial permeability
are regulated by commensal microbial signals, including
TLR2dependent redistribution of the tight-junction proteins to apical cellcell contacts59. Thus, the ability of IECs
to sense their microbial surroundings has an integral role
in regulating their barrier function.
Viability-associated PAMPs
(Vita-PAMPs). Members of a
special class of pathogenassociated molecular patterns
recognized by the innate
immune system to signify
microbial life. These patterns
differentiate dead and living
microorganisms to allow for
scaling of appropriate immune
responses based on the level of
threat the microbial signals
represents.
R E V IE W S
Innate immune regulation
IL-25,
IL-33,
TSLP
IL-13,
amphiregulin
Commensal
bacterium
IL-25
IFN,
TNF
IL-1,
IL-23
IL-17,
IL-22
TSLP,
TGF,
RA
IEL
sIgA
TSLP
APRIL,
BAFF
IL-7,
IL-15
IL-12
IL-10
ILC2
IL-25
ILC1
TSLP
TReg cell
DC
Lamina propria
TCR
MHC
Macrophage Monocyte
Basophil
progenitor
Peyers patch
or mesenteric
lymph node
Naive T cell
Type 2
MPP
Mast cell
Basophil
RA,
TGF
B cell
Basophil
IL-10,
RA,
TGF
TReg cell
Direct IEC eect
Indirect IEC eect
Immune response
Dierentiation
Figure 3 | IECs regulate innate and adaptive immunity. Intestinal epithelial cell (IEC)-derived cytokines interleukin25
Nature progenitors
Reviews | Immunology
(IL25) and thymic stromal lymphopoietin (TSLP) elicit the expansion and differentiation of basophil
and
multipotent progenitor type2 (type2MPP) cells, respectively. IL25, IL33 and TSLP stimulate group 2 innate lymphoid
cells (ILC2s), whereas IL25 suppresses innate lymphoid cell subset 1 (ILC1) and ILC3 function by limiting macrophage
production of pro-inflammatory cytokines IL1, IL12 and IL23. IECs condition dendritic cells (DCs) and macrophages
towards a tolerogenic phenotype through the production of TSLP, transforming growth factor (TGF) and retinoic acid
(RA). TheseDCs promote the differentiation of naive CD4+ Tcells into regulatory T (TReg) cells and the maturation of Bcells
into IgA-secreting plasma cells. Mucosal cell-derived DCs also imprint a gut-homing phenotype on primed Bcells and
Tcells through the production of RA. After trafficking to the intestine, TReg cells are expanded in number by macrophages
that are conditioned to produce IL10 by TSLP-mediated stimulation and through contact-dependent interactions with
IEC-expressed semaphorin 7A (SEMA7A). The production of a proliferation-inducing ligand (APRIL) and Bcell-activating
factor (BAFF) by IECs and by TSLP-stimulated macrophages and DCs promotes class-switch recombination and
the production of IgA by Bcells in the intestinal lamina propria. IEL, intra-epithelial lymphocyte; IFN, interferon;
sIgA, secretory IgA; TCR, Tcell receptor; TLA, thymus leukaemia antigen; TNF, tumour necrosis factor.
and myeloid cell phenotypes that promote the development of type2 cytokine responses at mucosal sites130133.
These cells include a distinct population of basophil progenitors and a population of multipotent progenitor cells,
which undergo extramedullary haematopoiesis and represent an innate link between IEC-derived signals and the
polarization of TH2 cell immune responses to helminths
and allergens132,133.
Innate lymphocyte function. In addition to the myeloid
cell and granulocyte populations, a recently identified
innate immune cell population of innate lymphoid cells
(ILCs) plays a crucial part in intestinal immune homeostasis. ILCs lack properties of adaptive lymphocytes, such
as recombined antigen-specific receptors134. They are
found at barrier surfaces, including mouse and human
lung 135, skin136 and intestine137, where they function
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N H o m e os tat i c I m m un e R e sRpEons
eS
s
V IE W
R E V IE W S
Class-switch recombination
(CSR). The process by which
proliferating Bcells rearrange
their DNA to switch from
expressing IgM (or another
class of immunoglobulin) to
expressing a different
immunoglobulin heavy-chain
constant region, thereby
producing antibody with
different effector functions.
Concluding remarks
Collectively, the studies highlighted in this Review demonstrate the diverse and multifaceted roles that IECs
have in the continuous maintenance of intestinal homeostasis. Through secretory epithelial cell responses and
the maintenance of a continuous cell layer, IECs effectively sustain a physical and biochemical barrier between
hosts and their environment. As cells forming a uniquely
adapted barrier surface, IECs actively respond to their
local environment through regulatory mechanisms that
earn IECs recognition as central mediators of microbial
and immune homeostasis in the intestine. As much of
what is understood of IEC function has been derived
from studies using mouse models, a future challenge
lies in the translation of this understanding into human
systems and the development of novel therapeutics for
targeting the pathways that contribute to human health.
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N H o m e os tat i c I m m un e R e sRpEons
eS
s
V IE W
29. Vaishnava,S. etal. The antibacterial lectin RegIII
promotes the spatial segregation of microbiota and
host in the intestine. Science 334, 255258 (2011).
In this study, the antimicrobial protein REGIII
isidentified as being necessary for the physical
separation of commensal bacteria from the surface
of the small intestinal epithelium, thus limiting the
activation of the intestinal immune response.
30. Meyer-Hoffert,U. etal. Secreted enteric antimicrobial
activity localises to the mucus surface layer. Gut 57,
764771 (2008).
31. Hampe,J. etal. A genome-wide association scan of
nonsynonymous SNPs identifies a susceptibility
variant for Crohn disease in ATG16L1. Nature Genet.
39, 207211 (2007).
32. Rioux,J.D. etal. Genome-wide association study
identifies new susceptibility loci for Crohn disease
andimplicates autophagy in disease pathogenesis.
Nature Genet. 39, 596604 (2007).
References 31 and 32 report the association
between genetic variants in the gene for the
autophagy protein ATG16L1 and Crohns
diseasesusceptibility, establishing a Crohns
disease-specific genetic link between IBD and
theautophagy pathway.
33. Cadwell,K. etal. A key role for autophagy and
theautophagy gene Atg16l1 in mouse and human
intestinal Paneth cells. Nature 456, 259263
(2008).
34. Kaser,A. etal. XBP1 links ER stress to intestinal
inflammation and confers genetic risk for human
inflammatory bowel disease. Cell 134, 743756
(2008).
35. Brandl,K. etal. Enhanced sensitivity to DSS colitis
caused by a hypomorphic Mbtps1 mutation disrupting
the ATF6driven unfolded protein response. Proc. Natl
Acad. Sci. USA 106, 33003305 (2009).
36. Cadwell,K. etal. Virus-plus-susceptibility gene
interaction determines Crohns disease gene Atg16L1
phenotypes in intestine. Cell 141, 11351145 (2010).
In this study, the interaction between
environmental exposures and genetic susceptibility
is shown to determine the penetrance of disease in
mouse models of intestinal inflammation.
37. Khor,B., Gardet,A. & Xavier,R.J. Genetics and
pathogenesis of inflammatory bowel disease. Nature
474, 307317 (2011).
38. Benjamin,J.L., Sumpter, R. Jr, Levine,B. &
Hooper,L.V. Intestinal epithelial autophagy is
essential for host defense against invasive bacteria.
Cell Host Microbe 13, 723734 (2013).
39. Adolph,T.E. etal. Paneth cells as a site of origin for
intestinal inflammation. Nature 503, 272276 (2013).
This study demonstrates interactions between the
regulation of the UPR and the autophagy pathway
in Paneth cells and supports a model in which
alterations in these two responses regulate the
development of Crohns disease.
40. Johansen,F.E. & Kaetzel,C.S. Regulation of the
polymeric immunoglobulin receptor and IgA
transport: new advances in environmental factors
thatstimulate pIgR expression and its role in
mucosalimmunity. Mucosal Immunol. 4, 598602
(2011).
41. Johansen,F.E. etal. Absence of epithelial
immunoglobulin a transport, with increased mucosal
leakiness, in polymeric immunoglobulin receptor/
secretory componentdeficient mice. J.Exp. Med.
190, 915922 (1999).
42. Shulzhenko,N. etal. Crosstalk between B
lymphocytes, microbiota and the intestinal epithelium
governs immunity versus metabolism in the gut.
Nature Med. 17, 15851593 (2011).
In this study, a compensatory response of IECs
inthe absence of adaptive IgA directed against
commensal bacteria is characterized by the
engagement of immune pathways and
dysregulation of lipid metabolism.
43. Suzuki,K. etal. Aberrant expansion of segmented
filamentous bacteria in IgA-deficient gut. Proc. Natl
Acad. Sci. USA 101, 19811986 (2004).
44. Mabbott,N.A., Donaldson,D.S., Ohno,H.,
Williams,I.R. & Mahajan,A. Microfold (M) cells:
important immunosurveillance posts in the intestinal
epithelium. Mucosal Immunol. 6, 666677 (2013).
45. Mowat,A.M. Anatomical basis of tolerance and
immunity to intestinal antigens. Nature Rev. Immunol.
3, 331341 (2003).
46. Hase,K. etal. Uptake through glycoprotein 2
ofFimH+ bacteria by M cells initiates mucosal
immune response. Nature 462, 226230 (2009).
R E V IE W S
89. Kumar,A. etal. The bacterial fermentation product
butyrate influences epithelial signaling via reactive
oxygen species-mediated changes in cullin1
neddylation. J.Immunol. 182, 538546 (2009).
90. Kondo,T., Kawai,T. & Akira,S. Dissecting negative
regulation of Toll-like receptor signaling. Trends
Immunol. 33, 449458 (2012).
91. Blander,J.M. & Sander,L.E. Beyond pattern
recognition: five immune checkpoints for scaling the
microbial threat. Nature Rev. Immunol. 12, 215225
(2012).
92. Gewirtz,A.T., Navas,T.A., Lyons,S., Godowski,P.J. &
Madara,J.L. Cutting edge: bacterial flagellin activates
basolaterally expressed TLR5 to induce epithelial
proinflammatory gene expression. J.Immunol. 167,
18821885 (2001).
93. Rhee,S.H. etal. Pathophysiological role of Toll-like
receptor 5 engagement by bacterial flagellin in
colonicinflammation. Proc. Natl Acad. Sci. USA 102,
1361013615 (2005).
94. Lee,J. etal. Maintenance of colonic homeostasis
bydistinctive apical TLR9 signalling in intestinal
epithelial cells. Nature Cell Biol. 8, 13271336 (2006).
95. Barnich,N., Aguirre,J.E., Reinecker,H.C., Xavier,R.
& Podolsky,D.K. Membrane recruitment of NOD2
inintestinal epithelial cells is essential for nuclear
factor-B activation in muramyl dipeptide recognition.
J.Cell Biol. 170, 2126 (2005).
96. Lipinski,S. etal. RNAi screening identifies mediators
of NOD2 signaling: Implications for spatial specificity
of MDP recognition. Proc. Natl Acad. Sci. USA 109,
2142621431 (2012).
97. Matzinger,P. The danger model: A renewed sense of
self. Science 296, 301305 (2002).
98. Sander,L.E. etal. Detection of prokaryotic mRNA
signifies microbial viability and promotes immunity.
Nature 474, 385389 (2011).
In this study, bacterial mRNA is identified as a
signal that enables the gauging of infectious risk
posed by live versus dead bacteria, exemplifying a
vita-PAMP.
99. Hooper,L.V., Stappenbeck,T.S., Hong,C.V. &
Gordon,J.I. Angiogenins: a new class of microbicidal
proteins involved in innate immunity. Nature Immunol.
4, 269273 (2003).
100. Kobayashi,K.S. etal. Nod2dependent regulation of
innate and adaptive immunity in the intestinal tract.
Science 307, 731734 (2005).
101. Vaishnava,S., Behrendt,C.L., Ismail,A.S.,
Eckmann,L. & Hooper,L.V. Paneth cells directly
sense gut commensals and maintain homeostasis at
the intestinal host-microbial interface. Proc. Natl
Acad. Sci. USA 105, 2085820863 (2008).
102. Bruno,M.E.C., Frantz,A.L., Rogier,E.W.,
Johansen,F.E. & Kaetzel,C.S. Regulation of the
polymeric immunoglobulin receptor by the classical
and alternative NFB pathways in intestinal
epithelial cells. Mucosal Immunol. 4, 468478
(2011).
103. Rimoldi,M. etal. Intestinal immune homeostasis is
regulated by the crosstalk between epithelial cells and
dendritic cells. Nature Immunol. 6, 507514 (2005).
This study describes the conditioning of mucosal
DCs towards a non-inflammatory phenotype by
interactions with IECs, representing a mechanism
for the indirect IEC-mediated regulation of
adaptive immune cell priming.
104. Zeuthen,L.H., Fink,L.N. & Frokiaer,H. Epithelial
cells prime the immune response to an array of gutderived commensals towards a tolerogenic phenotype
through distinct actions of thymic stromal
lymphopoietin and transforming growth factor.
Immunology 123, 197208 (2008).
105. Zaph,C. etal. Epithelial-cell-intrinsic IKK expression
regulates intestinal immune homeostasis. Nature
446, 552556 (2007).
This study demonstrates a crucial role for
IEC-intrinsic NF-B signalling and the production
of the cytokine TSLPthymic stromal lymphopoietin
in regulating intestinal immune responses and
coordinating anti-helminth immunity.
106. Atarashi,K. etal. Induction of colonic regulatory T
cells by indigenous Clostridium species. Science 331,
337341 (2011).
107. Zaph,C. etal. Commensal-dependent expression of
IL25 regulates the IL23IL17 axis in the intestine.
J.Exp. Med. 205, 21912198 (2008).
108. He,B. etal. Intestinal bacteria trigger T cellindependent immunoglobulin A2 class switching by
inducing epithelial-cell secretion of the cytokine
APRIL. Immunity 26, 812826 (2007).
www.nature.com/reviews/immunol
2014 Macmillan Publishers Limited. All rights reserved
F O C U S O N ho m e os tat i c i m m un e r e sRpEons
eS
s
V IE W
155. Hanash,A.M. etal. Interleukin22 protects intestinal
stem cells from immune-mediated tissue damage and
regulates sensitivity to graft versus host disease.
Immunity 37, 339350 (2012).
156. Kirchberger,S. etal. Innate lymphoid cells sustain
colon cancer through production of interleukin22 in
a mouse model. J.Exp. Med. 210, 917931 (2013).
157. Muoz,M. etal. Interleukin (IL)-23 mediates Toxoplasma
gondiiinduced immunopathology in the gut via
matrixmetalloproteinase2 and IL22 but independent
of IL17. J.Exp. Med. 206, 30473059 (2009).
158. Buonocore,S. etal. Innate lymphoid cells drive
interleukin23dependent innate intestinal pathology.
Nature 464, 13711375 (2010).
159. Geremia,A. etal. IL23responsive innate lymphoid
cells are increased in inflammatory bowel disease.
J.Exp. Med. 208, 11271133 (2011).
160. Coccia,M. etal. IL1 mediates chronic intestinal
inflammation by promoting the accumulation of
IL17A secreting innate lymphoid cells and CD4+
Th17 cells. J.Exp. Med. 209, 15951609 (2012).
161. Sawa,S. etal. RORt+ innate lymphoid cells regulate
intestinal homeostasis by integrating negative signals
from the symbiotic microbiota. Nature Immunol. 12,
320326 (2011).
162. Vonarbourg,C. etal. Regulated expression of nuclear
receptor RORt confers distinct functional fates to NK
cell receptor-expressing RORt+ innate lymphocytes.
Immunity 33, 736751 (2010).
163. Satoh-Takayama,N. etal. Microbial flora drives
interleukin 22 production in intestinal NKp46+ cells
that provide innate mucosal immune defense.
Immunity 29, 958970 (2008).
164. Yu,Q. etal. MyD88dependent signaling for IL15
production plays an important role in maintenance
of CD8 TCR and TCR intestinal intraepithelial
lymphocytes. J.Immunol. 176, 61806185 (2006).
165. Cheroutre,H., Lambolez,F. & Mucida,D. The light and
dark sides of intestinal intraepithelial lymphocytes.
Nature Rev. Immunol. 11, 445456 (2011).
166. Edelblum,K.L. etal. Dynamic migration of
intraepithelial lymphocytes requires occludin.
Proc. Natl Acad. Sci. USA 109, 70977102 (2012).
167. Ismail,A.S. etal. intraepithelial lymphocytes are
essential mediators of host-microbial homeostasis at
the intestinal mucosal surface. Proc. Natl Acad. Sci.
USA 108, 87438748 (2011).
168. Mucida,D. etal. Transcriptional reprogramming
of mature CD4+ helper Tcells generates distinct
MHC classIIrestricted cytotoxic T lymphocytes.
Nature Immunol. 14, 281289 (2013).
169. Gebhardt,T., Mueller,S.N., Heath,W.R. &
Carbone,F.R. Peripheral tissue surveillance and
residency by memory Tcells. Trends Immunol. 34,
2732 (2013).
Acknowledgements
SUPPLEMENTARY INFORMATION
See online article: S1 (table)
ALL LINKS ARE ACTIVE IN THE ONLINE PDF