-No plagiarism, the paper will be run through a plagiarism software program.
-At least 8 pages, not including references/citation pages
-Try to have 40 primary references within the past 5 years
-Please create subheadings such as Abstract (doesn’t need to be a whole page), clinical factors, demographics, and so on.
-Attached are some sample Article Review papers that the paper should have the same style.
A review of major Crohn’s disease susceptibility genes and their role
in disease pathogenesis
Meghan Barrett · Sathees B. Chandra
Genes & Genomics (2011) 33: 317-325
Crohn’s disease (CD) is a chronic inflammatory bowel disease
whose relevance is increasing in industrialized society. Recent
genome wide association studies revealed over seventy one
loci associated with disease penetrance. Several variants that
increase disease risk encode for altered proteins that diminish
bacterial host defense. NOD2 alters intracellular bacterial sensing while ATG16L1 is thought to diminish bacterial clearance
by impairing autophagy. Additionally, changes in the IBD5
locus are thought to diminish barrier function. Alternatively,
recent data indicate a gain of function genetic variant of IL23R
is protective amongst European CD patients. These recent genetic discoveries contradict historical theories that Crohn’s disease results from overactive auto-aggressive responses. Rather,
new genetic data suggest disease-associated variants encode
for dysfunctional proteins that diminish essential innate immune responses against commensal organisms. This review
provides an overview of these critical discoveries and places
them in their biological context.
Keywords ATG16L1; Crohn’s disease; Genetics; IBD5 locus; IL23R; NOD2
Crohn’s disease (CD) is grouped under a larger classification
of disorders known as inflammatory bowel disease (IBD)
which includes ulcerative colitis, collagenous colitis and microscopic colitis (Tysk et al., 1988). Demographic features of
CD suggest it is a disease of the modern era. Its prevalence
increased dramatically as man moved into industrial,
M. Barrett · S. B. Chandra( )
Dept of Biological, Chemical and Physical Sciences, Roosevelt
University, Chicago, USA
“westernized” environments (Karlinger et al., 2000). The current prevalence is estimated to be about 1 in 1000 in western
countries (Hugot et al., 2003) or 1.4 million cases in the U.S.
(Hugot et al.; 2003, Loftus, 2004). Crohn’s disease affects
slightly more females than males and has a mean age diagnosis
between 33 and 45 years of age (Loftus, 2004; Lichtenstein
et al., 2009). Risk factors for CD include genes and
environment. Greater degrees of genetic susceptibility occur
amongst Caucasians of Eastern Europe descent. Specifically,
rates are high amongst Ashkenazi Jews where prevalence is
six to nine times greater than the general European Caucasian
population (Church, 2001; Hugot et al., 2001). Disease penetrance increases as genetically similar populations (e.g.
Ashkenazi Jews) move from less industrialized to more industrialized environments (Karlinger et al., 2000). As susceptibility loci are identified, it is apparent that those with greater
genetic risk also present with more severe disease (Podolsky,
Crohn’s disease is a chronic condition characterized by transmural patchy inflammation throughout the intestinal track from
the mouth to anus (Xavier and Podolsky, 2007). The disorder
commonly targets the ileum and colon where exposure to levels of anaerobic bacteria is greatest (Repnik and Potocniki,
2010). Chronic inflammation leads to deep ulcerations, penetrating fistulas, and circumferential rings of fibrosis (scarring)
resulting in strictures that obstruct the intestine (Podolsky,
2002). In fact, strictures commonly impede flow of bacteria
from one segment to the other causing more severe ulceration
and fistula formation in the proximal segment being
obstructed. Treatments that lower the bacterial counts in these
obstructed segments (e.g. antibiotics) help resolve tissue inflammation, ulceration, and fistula formation (Lichtenstein et
al., 2009). The clinical effects of persistent mucosal inflammation include abdominal pain, bleeding, diarrhea, and
weight loss (Repnik and Potocniki, 2010). Chronic inflammation increases the risk of cancer in both the small bowel
318 Genes & Genomics (2011) 33: 317-325
and colon. Extraintestinal manifestations such as arthritis,
uveitis (eye inflammation), severe skin rashes, and growth retardation occur in over 20% of the patients. No medical cure
is currently known. Historically, surgery was required for 2/3
of patients affected by the disease (Lichtenstein et al., 2009;
Nell et al., 2010). Newer therapies such as anti-tumor necrosis
factor (TNF) antibodies reduce surgical risk (Van Assche,
2008). Overall, disease manifestations severely reduce patients’ quality of life (Podolsky, 2002). The current review
will focus on the genetic factors of the IBD-5 locus, HLA region, Nod2/Card15, ATG16L1, and IL-23R and their influence
on penetrance and pathogenesis of CD.
To appreciate the effects of recently described genes on inflammation in Crohn’s disease, one must understand new revelations involving the intestinal commensal flora (Xavier and
Podolsky 2005). The commensal flora is the composition of
bacteria contained within our intestines. The intestine contains
over 1,000 types of bacteria (Stappenbeck et al., 2010) dominated by firmicutes and bacteroides (Nell et al., 2010).
Typically those bacteria are non-pathogenic. Models suggest
that the commensal flora is imprinted from birth (Eckburg et
al. 2005) but is influenced by diet, antibiotics and infection.
For example, a study by Hildebrandt shows that high fat diets
change the constituents of the flora (Hildebrandt 2009).
Molodecky and Kaplan (2010) reported that antibiotics disrupted the development of tolerance to enteric bacteria
(bacteria in the gut). Although commensal bacteria are normally contained within the bowel lumen, in CD, defects in
the innate immune system allow these bacteria to penetrate
beyond the intestinal epithelial barrier (Beutler, 2001; Fritz,
2011). Once allowed access to the underlying submucosa,
these “non-pathogenic” bacteria can cause inflammation
(Stappenbeck et al., 2010).
The tissue inflammation seen in CD is typical of chronic inflammatory response to intracellular infections. In CD, tissue
inflammation is characterized by activated cells of the innate
immune system (e.g. macrophages, dendritic cells etc.) (Xavier
and Podolsky, 2005). When activated against intracellular infections that resist clearance, swirls of activated macrophages
and fibroblasts isolate the infection by forming circular pockets
of cells called granulomas (Podolsky, 2002). Granulomas are
seen in infections such as tuberculosis, schistosomiasis and
Leischmania. These intracellar infections cause chronic inflammation when they are not inside macrophages. The macrophages react by releasing inflammatory mediators. The chronic
release of inflammatory mediators allows the immune system
to isolate the infected macrophages within granulomas. This
is relevant as mutations associated with CD encode for proteins needed to form granulomas. Thus, chronic granulomatous
defense responses occur despite the lack of pathogenic
Genetics of Crohn’s Disease
The complex etiology of CD is a result of an intricate interaction of many genes. Fifteen percent of CD patients have
a family history of Crohn’s disease and monozygotic twin
studies report concordance rates of thirty six percent (Church,
2001; Matthew, 2008; Stappenbeck et al., 2010; Van
Limbergen et al., 2009). For example, as early as 1988, Tysk
et al found a concordance with CD in 8 of 18 monozygotic
twins but only 1 of 26 dizygotic twins (Mizoguchi et al.,
2007). As a result of long suspected and high genetic contribution to the development of Crohn’s disease, much research
has focused on identifying the susceptibility genes of CD.
Genome scans have identified at risk genes on chromosomes
1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, and
21 (Hugot et al., 2003; Franke et al., 2010). The IBD1 locus
on chromosome 16, the IBD2 locus on chromosome 12 and
the IBD3 locus on chromosome 6 were identified by genome-wide linkage analysis to be significantly linked to CD
(Church, 2001; Hugot et al., 2001). The identification of these
loci represents major advances in the study of Crohn’s disease
genetics. Advancements in the discovery of many susceptibility genes for CD were due to genome wide association studies (GWAS) as well.
The first gene identified as associated with Crohn’s disease
was NOD2 (Hugot et al., 2001; Ogura et al., 2001). Since
reported simultaneously by Hugot et al. and Ogura et al., studies suggest associations with more than seventy one additional
loci (Franke et al., 2010). Prior to the recent discovery of new
susceptibility loci by Franke and colleagues, geneticists believed that only 20% of the total genetic variance was understood for the disease (Barrett et al., 2008; Fransen et al., 2010;
Stappenbeck et al., 2010). Following the identification of the
39 new susceptibility loci, Franke and colleagues suggest that
23.2% of Crohn’s disease heritability can now be explained
(Franke et al., 2010). As Van Limbergen and colleagues described, Crohn’s disease-associated loci encode for genes involved in innate pattern recognition (e.g. NOD2/CARD15), autophagy (ATG16L1, IRGM), the differentiation of Th17- T
lymphocytes (IL-23R), the maintenance of epithelial barrier integrity (IBD5 locus), and the coordination of secondary
(adaptive) immune responses (HLA-region) (Van Limbergen
et al., 2009). While many CD associated loci are known, for
the purposes of this review, genes will be highlighted that exhibit strong associations with aberrant immune responses in
CD, namely those encoding NOD2, ATG16L1, IL-23R, IBD5
locus and IBD3 locus (encoding HLA-region genes).
NOD2/CARD15, identified in 2001, has the strongest association for Crohn’s disease with 30% to 50% of patients carrying
Genes & Genomics (2011) 33: 317-325 319
a NOD2 mutation on at least one allele (Noguchi et al., 2009;
Hugot et al., 2003). Located on chromosome 16q, NOD2 is
composed of 11 exons, encodes for 1040 amino acids, and
consists of two caspase recruitment domains, a nucleotide
binding domain, and the leucine rich repeat domain (LRR)
(Hugot et al., 2001; Hugot et al., 2003). The most common
mutations of NOD2 are found in the LRR (Noguchi et al.,
2009; Hugot et al., 2001) and include the polymorphisms
rs2066844, rs2066845, and rs2066847 (Hamm et al., 2010).
Rs2066844 results in an amino acid substitution Arg702Trp,
rs2066845 encodes an amino acid substitution Gly908Arg and
the rs2066847 polymorphism “truncates” the terminal 33 amino acids of LRR resulting in Leu1007fsinsC (Duerr, 2007;
Hamm et al., 2010). When individuals are heterozygote for
one of these polymorphisms, the risk of CD increases 2-4-fold
(Hugot et al., 2003; Lee and Parkes, 2011). However, compared to non carriers, there is a 15-40 fold increased risk of
developing CD for people heterozygous for more than one of
the polymorphisms or if they are homozygous for one polymorphism (Lee and Parkes, 2011). Individuals with two NOD2
mutations exhibit symptoms at a younger age. Another mutation associated with NOD2 is the 3020insC. This mutation
causes a partial deletion of the terminal LRR domain. Patients
homozygous for the insertion manifest more severe symptoms
and carry an increased risk for ileal narrowing and surgery
(Noguchi et al., 2009).
Explorations into how NOD2 mutations cause disease manifestations require understanding of its expression pattern and
function in cells. Recognition of pathogenic bacteria and virus
requires specific host pattern recognition receptors (PRRs) recognizing pathogen-associated molecular patterns (PAMPs)
(Sabbah et al., 2009). Until recently most PRRs were considered to be membrane-bound receptors such as Toll-like receptors (TLRs). More recently a group of intracellular PRRs,
similar to plant R proteins, were discovered in mammals
(Lecat et al., 2010). Both Nod2 and plant R proteins are characterized by a N-terminal effector domain, a centrally located
nucleotide-binding domain (NBD) and multiple leucine-rich
repeats (LRRs) in their C-terminal end (Lecat et al., 2010).
Nod2 is restricted to myelomonocytic cells (monocytes/macrophages, granulocytes), dendritic cells and intestinal epithelial
cells (Gutierrez et al., 2002; Ogura et al., 2003). NOD2 encodes an intracellular sensor that recognizes viral and microbial
components (Church, 2001; Noguchi et al., 2009;
Palomino-Morales et al., 2009; Stappenbeck et al., 2010).).
Viral ssRNA activates NOD2 which triggers phosphorylation
of the transcription factor interferon response factor-3 (IRF3)
(Sabbah et al, 2009). Nuclear translocation of IRF3 leads to
transactivation of genes that encode interferons such as IFN-β
(Lecat et al., 2010; Sabbah et al., 2009). IFN-β mediates innate
immune responses to viral agents. Antiviral responses rely on
NOD2 and mitochondrial antiviral signaling (MAVS) protein
interaction (Lecat et al., 2010; Sabbah et al, 2009). Following
viral infection, NOD2 translocates into the mitochondria and
associates with MAVS protein (Sabbah et al, 2009). While
viral ssRNA trigger NOD2 to activate IRF3, bacterial products
stimulate NOD2 to activate NF-κB.
The leucine rich repeat (LRR) domain of NOD2/CARD15
recognizes invading bacteria through identification of muramyl
dipeptide (MDP) (Van Limbergen et al., 2009). MDP is a fragment of peptidoglycan present in the bacteria cell walls of
both gram-negative and gram-positive bacteria (Stappenbeck
et al., 2010; Van Limbergen et al., 2009; Noguchi et al., 2009).
Recognition of MDP is therefore part of an overall “danger
signal” used by the innate immune system to alert other cells
that bacterial invasion is occurring (Matzinger, 2002). When
MDP binds the LRR of NOD2, NOD2 triggers autophagy
(described below) and enhances pro-inflammatory signaling
through activators of the innate immune system (Toll-like receptor pathways) and a regulator of inflammation, NFκB
(Stappenbeck et al., 2010). Mutations in the LRR domain of
NOD2/CARD15 result in the inability of cells to recognize
MDP. The ineffective recognition of MDP leads to an attenuated immune response to bacteria. Variants of NOD2 that alter
the LRR domain hinder the formation of NOD2 dimers which
in turn inhibit NFκB activation (Cadwell, 2010). Wild type
NOD2 enhances NFκB signaling. NFκB is a transcription factor that initiates transcription of a wide range of inflammatory
genes important for bacterial clearance (Hu et al., 2010).
Interestingly, Kosovac and colleagues found that when tissue
from NOD2 mutant CD patients was analyzed, tissue levels
of NFκB were increased (Kosovac et al,. 2010). The paradoxical increase in NFκB is thought to occur as a physiologic
response of the non-mutant cells to invasive bacteria that penetrate past dysfunctional Paneth cells and macrophages containing mutant NOD2.
While NOD2 affects NFκB signaling, alterations in IL-10
production represent an important effect of NOD2 mutation
on immune homeostasis in the intestine as well. IL-10 is an
important regulatory cytokine in the immune system, frequently seen when inflammatory responses are suppressed
(Berg et al., 1996). The absence of IL-10 leads to chronic
colitis in mice. Thus, it was curious when a NOD2 variant
was found to affect IL-10 signaling by Noguchi and colleagues
(Noguchi et al., 2009). Insertion mutation at nucleotide 3020
caused partial deletion of LRR. Humans with homozygous
NOD2 mutations of 3020insC were found to have more severe
disease with a higher risk for ileal narrowing and surgery.
They were also found to have lower levels of IL-10 and TNF.
Furthermore, cell lines studies showed that 3020insC Nod2
suppressed IL10 transcription by about 50% in all conditions.
Thus, mutant NOD2 may affect the immune system by diminishing a critical cytokine needed to reduce inflammation.
Autophagy is important in the mediation of the inflammatory
320 Genes & Genomics (2011) 33: 317-325
immune response (Stappenbeck et al., 2010). Autophagy operates by capturing organelles and cytoplasm within an autophagosome (a membrane bound organelle) (Cadwell, 2010). A
lysosome then eradicates the invading microorganisms
through the process xenophagy (Levine, 2005; Van
Limbergen et al., 2009). Disruption of this process leads to
production of inflammatory cytokines (Stappenbeck et al.,
2010). Therefore, reduced autophagy may lead to the poor
response to intracellular bacteria in CD (Matthew, 2008). For
example, NOD2 mutations seem to be related to autophagy.
Some NOD2 mutations retain the gene ATG16L1 in the cytosol (Cadwell, 2010). When this ATG16L1 gene is retained,
the recruitment of autophagy machinery to bacteria is
prevented. Therefore, mutations in the ATG16L1 gene and
other autophagy genes result in intracellular pathogens’ prolonged survival (Lee and Parkes, 2011). Both Cooney et al
and Travassos et al demonstrate that the activation of autophagy through the presence of MDP does not occur in CD patients with mutations in NOD2 risk alleles or ATG16L1
(Travassos et al., 2010). Recent studies also report that variants of the autophagy gene IRGM contributes to susceptibility
to Crohn’s disease (Xavier and Podolsky, 2007). Located on
chromosome 5q33.1, this variant associated with CD is a
20-kb deletion polymorphism immediately upstream of IRGM
(McCarroll et al., 2010; Prescott et al., 2010).
As previously mentioned, ATG16L1 (autophagy-related
16-like 1) is another CD susceptibility gene. The gene is located on the 2q37.1. (Newman et al., 2009). The most common ATG16L1 gene variant is the rs2241880 in the G allele
(Hampe et al., 2007; Palomino-Morales et al., 2009). The
ATG16L1 risk allele causes a change in the reading frame
during translation of exon 9 that leads to an amino acid exchange Thr300Ala (Cadwell et al., 2008; Hampe et al., 2007;
Matthew, 2008; Duerr, 2007). While the function of the amino
acid substitution is not fully understood, Palomino-Morales
and colleagues suggest that it alters phagosomes and prolongs
immune activation (Palomino-Morales et al., 2009). Specifically, ATG16L1 mutations cause disordered production of key
anti-microbial peptides made in Paneth cells in the lining of
the intestine (Cadwell et al., 2008). For example, Cadwell
and colleagues showed that, in the epithelium of the ileum,
ATG16L1 and ATG5 are crucial for Paneth cell and macrophage biology (Cadwell et al., 2010). Also in relation to
the epithelial cells, Kuballa and colleagues found that
ATG16L1 variants inhibit the ability of autophagosomes to
capture internalized Salmonella (Kuballa et al., 2008). In addition, defects in the autophagy pathway caused by the
ATG16L1 mutations in macrophages impair bacterial
clearance. Thus, one may propose that ATG16L1 increases
the risk of CD by impairing intracellular bacterial handling
in macrophages as well as by impairing the altered exocytosis of anti-microbial peptides made by Paneth cells (Van
Limbergen et al., 2009).
Chronic inflammation in CD contains cells that overproduce
cytokines in the T helper 1 (Th1) and T helper 17 (Th17)
pathways (Maynard and Weaver, 2009). Th1 cells require
IL-12 (made up of p40 and p35 subunits) whereas Th17 cells
require IL-23 comprised of the IL-12 p40 subunit combined
with IL23p19 (Lakatos et al., 2008; Kobayashi et al., 2008).
The IL23 cytokine contributes to the maintenance and development of TH17 cells (Lee and Parkes, 2011). TH17 cells express cytokines including IL17 and IL22 (Brand, 2009). The
primary cytokine produced by TH17 cells, IL17A, increases
the production of pro-inflammatory chemokines and cytokines.
As a result, IL17A induces pro-inflammatory effects on macrophages, fibroblasts, intestinal epithelial cells, and endothelial
cells (Brand, 2009). IL17A also activates the pro-inflammatory
transcription factor, NFκB. TH17 cells express IL22 cytokine
which combines with IL17A to increase production of antimicrobial peptides (Brand, 2009).
Interestingly, data regarding the role of IL-23R in CD has
been conflicting. Whereas some data suggest variants of
IL-23R enhances CD, other, more recent, genetic results suggest IL-23R mutations may be protective (Duerr et al., 2006;
Glas et al., 2008; Lin et al., 2010; Lakatos et al., 2008; Coterill
et al., 2010). IL23R is a locus which encodes the receptor
for the IL23 cytokine (Duerr et al., 2006). Measurements of
cytokine values in inflamed CD tissue has revealed overproduction of cytokines associated with T lymphocytes normally activated during host defense responses to intracellular
pathogens (Maynard and Weaver, 2009). IL-23R was first reported to be associated with Crohn’s disease in 2006 by Duerr
et al using a GWAS. In 2006 Duerr et al. reported that the
disease associated IL23R variant rs11209026 was actually protective in CD (Duerr et al., 2006). These data were confirmed
by Glas (Glas et al., 2008), Lacher (Lacher, 2010), Lin (Lin
et al., 2010), Lakatos (Lakatos et al., 2008), and Coterill
(Coterill et al., 2010). In these studies, the groups found that
amongst European CD patients (pediatric and adult), the glutamine allele of Arg381Gln had a lower allele frequency in CD
compared to controls. Together these data suggested that
Arg381Gln conferred strong protection against CD. Glas et
al reported that an IL23R variant, rs1004819, was increased
in patients with ileal CD (Glas et al., 2008). Einarsdottir and
colleagues also reported strong association for the IL23R variant rs1004819 with Crohn’s disease in their study of Swedish,
Finnish, Hungarian, and Italian populations (Einarsdottir et al.,
2009). Although the functional consequence of these findings
remains unclear, it is attractive to speculate that IL23R is protective because enhanced inflammatory responses increase host
defenses thereby limiting bacterial penetration and diminishing
the risks of CD.
The story of discovery for the IBD5 disease susceptibility lo-
Genes & Genomics (2011) 33: 317-325 321
cus illustrates how enhanced risk associated with a relatively
large area of the genome can lead to information suggesting
functional relevance. Using a genome wide search approach,
Rioux et al reported in 2000 a novel locus which conferred
enhanced susceptibility to Crohn’s disease amongst Canadians
(Rioux et al., 2000). The genetic association between the IBD5
locus and CD was first detected as a cluster of immunoregulatory cytokine genes 18 cM in length on chromosome 5
(5q31) (Rioux et al., 2000). The five genes IGR2096,
IGR2198, OCTN2, IGR2230, and OCTN1, have since been
identified with strong linkage disequilibrium in patients with
Crohn’s disease (Noble et al., 2005). Peltekova and colleagues
resequenced these five genes within the IBD5 locus and identified ten new SNPs. Amongst the ten SNPs; were SLC22A4
and SLC22A5 that encode for transmembrane sodium-dependent carnitine and sodium-independent organic cation transporters OCTN1 and OCTN2, respectively (Peltekova et al.,
2004). The SLC22A4 variant is a C to T transversion leading
to a leucine to phenylalanine substitution (L503F). The
SLC22A5 variant occurs in a promoter region that binds heat
shock proteins (HSPs). As HSPs are released in cells undergoing oxidative stress, the variant is important in regulation
of cellular responses to infectious stress. The organic cation
transporter encoded by OCTN1 and OCTN2 are carnitine and
cation transporters (Beutler, 2001).One theory of why OCTN1
and OCTN2 are related to disease activity has to do with their
role in maintaining barrier function in the intestine. The transporters are known to function in a cellular homeostasis function by importing and exporting cationic toxins, xenobiotic
molecules and neurotransmitters across the cell membrane
(Reinhard and Rioux, 2006). Thus, these mutations may affect
OCTN1 transporter function by reducing uptake of important
biologic compounds (e.g. neurotransmitters) while increasing
uptake of toxins, such as putrescine, derived from bacterial
catabolism. In addition, reduced carnitine uptake may attenuate
oxygen burst-mediated pathogen killing in intestinal barrier
cells (Ramsay 2000).The notion that OCTN1 and OCTN2 polymorphisms change intestinal fatty acid-oxidation has been
shown in animal models to cause colitis triggered by bacterial
metabolites (Roediger and Nance, 1986). Thus, the identification of IBD5 as a disease susceptibility locus in CD is
further evidence that essential properties of the mucosal host
defense response to local bacteria may be impaired. Loss of
optimal barrier function in this case may combine with enhanced uptake of injurious toxins to disrupt the epithelial layer,
promote bacterial transmigration and initiate robust inflammatory responses within innate and acquired elements of
the systemic immune system.
HLA region genes
Chromosome 6p (IBD3) contains the human leukocyte antigen
(HLA) genes that met criteria for genome-wide significance
in the meta-analysis by van Heel and collegues (van Heel et
al, 2004). In IBD, HLA-DRB1 exhibits the strongest associations observed between HLA-DRB1*0103 and colonic CD and
even more so with severe, extensive UC in Caucasians (Fisher
et al., 2008). HLA-DRB1*07 is most consistently replicated
in association with ileal (distal small bowel) CD (Fernando
et al., 2008). Extensive pooled analysis by Fernando and colleagues recently confirmed significant association signals arising from alleles/haplotypes related to HLA-DRB1*0103,
HLA-DRB1*04, HLA-DR7, and HLA-DRB3*0301. In addition, these authors described association with HLA-B18,
HLA-B21, HLA-DR6 (encompassing HLA-DRB1*1401),
HLA-DR8 (including HLA-DRB1*0802 and *0803), and
HLA-DR10 (Fernando et al., 2008). Together these studies
suggest that specific HLA genes (mostly encoding for class
II MHC molecules) influence clinical outcomes such as tissue
distribution and severity.
The recent developments in the genetics on CD have been
timely and certainly paradigm-shifting. In reviews written as
recently as the year 2000 (Karlinger et al., 2000), CD was
thought to occur as follows “If an individual has a genetic
susceptibility to infections, the down regulation of an inflammation in the bowel wall does not occur in a proper way.
This initiates the auto-immune process which is a self-increasing cycle”. The prediction was that enhanced inflammatory
cytokine levels detected in CD patients were the direct consequence of genetic alterations. More recent studies suggest
a different pathogenesis. Results of newly discovered genetic
alterations suggest deficiencies in innate immune responses
underly IBD pathogenesis. Figure 1 portrays the immune effects of CD-associated genetic alterations in NOD2, ATG16L1,
IBD5, IL23R, and HLA region. In general, functional studies
indicate that several CD-associated mutations impair normal
host responses to commensal flora resulting in poor barrier
function and attenuated clearance of nonpathogenic enteric
bacteria. Studies in mice and human with NOD2 and ATG16L1
mutations suggest that these mutations diminish essential intracellular clearance of organisms through autophagy (Fitz et al.,
2011). These organisms are contained in the commensal flora.
As we understand the role of the commensal flora in biology
it appears likely that it shapes many of the innate and adaptive
immune responses needed for health (Eckburg et al., 2005).
In addition to gene variants altering the innate and adaptive
immune response, mutations in susceptibility loci, such as the
IBD5 locus, are thought to result in diminished barrier
function. Variants in the IBD5 locus increase the uptake of
toxins associated with bacterial catabolism in the epithelial
layer. Genes on chromosome 6p (IBD3) encoding for HLA
molecules have been associated with distinct disease manifestations (e.g. colonic or small bowel ileal disease). At this time,
322 Genes & Genomics (2011) 33: 317-325
Figure 1. Impact of CD mutations on mucosal host defenses. Shown are proposed mechanisms of known CD mutations and their effect
on mucosal immune responses. Shown on the right are specific impacts of mutations on host defenses. Mutations associated with increased
CD activity include: NOD2 (1), ATG16L1 (2), IBD5 Locus (4), and HLA region genes (5). Shown in the figure are locations where mutations
impact mucosal host defenses. Mutations that are protective in CD include IL23R (3).
it is unclear how alterations in antigen presentation affect immune responses but it is possible that expression of distinct
MHC mol ecules alter immune responses to groups of bacteria.
Additionally, CD susceptibility genes have been identified that
are associated with differentiation of Th17-T lymphocytes.
Specifically, a genetic variant of IL23R is protective amongst
European CD patients. The protective effect is linked to increased production of IL-17 from effector T cells (Duerr et
al., 2006). As more genes are identified, the picture for CD
pathogenesis comes into focus. Genetic data emerging from
human studies informs researchers how genes interact with
commensal flora, with each other and with innate and adaptive
immune systems in this multigenic disorder. Several questions
persist. First, what is the functional interplay between the numerous genes associated with Crohn’s disease? What were the
selective pressures that led to the incorporation of these mutations into our genome? Lastly, how has our modern society
(diet, stress, and antibiotic usage) led to the enhanced prevalence of such a disabling illnesses. Through further research,
we hope to find answers to these questions and hope to move
closer to an eventual cure.
Acknowledgements The authors wish to thank Dr. Terrence
Barrett, Northwestern University Medical School for review
of the manuscript and insightful discussion of its content.
Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD
et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn’s disease. Nat. Gen. 40: 955-962
Berg DJ, Davidson N, Kühn R, Müller W, Menon S, Holland G,
Genes & Genomics (2011) 33: 317-325 323
Thompson-Snipes L, Leach MW, Rennick D (1996) Enterocolitis
and colon cancer in interleukin-10-deficient mice are associated
with aberrant cytokine production and CD4(+) TH1-like
responses. J. Clin. Invest. 98: 1010-20.
Beutler B (2001) Autoimmunity and Apoptosis: the Crohn’s
connection. Immunity 15: 5-14.
Brand S (2009) Crohn’s disease: Th1, Th17 or both? The change of
a paradigm: new immunological and genetic insights implicate
Th17 cells in the pathogenesis of Crohn’s disease. Gut.
Burckhardt G and Wolff N. (2000) Structure of renal organic anion
and cation transporters. Am. J. Physiol. Renal. Physiol. 278:
Cadwell K (2010) Crohn’s Disease Susceptibility Gene Interactions,
a NOD to the Newcomer ATG16L1. Gastroenterology. 139:
Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, et al. (2008) A
key role for autophagy and the autophagy gene Atg16l1 in mouse
and human intestinal Paneth cells. Nature 456: 259-63
Cadwell K, Patel KK, Komatsu M, Virgin HW 4th & Stappenbeck,
TS (2009) A common role for Atg16L1, Atg5 and Atg7 in small
intestinal Paneth cells and Crohn’s disease. Autophagy 5: 250-2.
Cadwell K, Patel K, Maloney N, Liu TC, NG A, Storer C, Head
R, Xavier R, Stappenbeck T, and Virgin H. (2010)
Virus-Plus-Susceptibility Gene Interaction Determines Crohn’s
Disease Gene Atg16L1 Phenotypes in Intestine. Cell 141:
Church J (2001) Molecular Genetics and Crohn’s Disease. Surgical
Clinics of North America 81.
Cotterill L, Payne D, Levinson S, McLaughlin J, Wesley E, Feeney
M, Durbin H, Lal S, Makin A, Campbell S, et al. (2010)
Replication and meta-analysis of 13,000 cases defines the risk
for interleukin-23 receptor and autophagy-related 16-like 1 variants in Crohn’s disease. J Gastroenterol 24: 297-302.
Csöngei V, Járomi L, Sáfrány E, Sipeky C, Magyari L, Faragó B,
Bene J, Polgár N, Lakner L, Sarlós P (2010) Interaction of the
major inflammatory bowel disease susceptibility alleles in Crohn’s
disease patients. World. J. Gastroenterol. 16: 176-83.
Deretic V, Master S, and Singh S (2008) Autophagy gives a nod
and a wink to the inflammasome and Paneth cells in Crohn’s
disease. Dev. Cell. 15; 641-2.
Duerr R et al. (2006) A Genome-Wide Association Study Identifies
IL23R as an Inflammatory Bowel Disease Gene. Science 314:
Duerr R (2007) Genome-Wide Association Studies Herald a New Era
of Rapid Discoveries in Inflammatory Bowel Disease Research.
Gastroenterology 132: 2045-2062.
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent
M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
Einarsdottir E, Koskinen LL, Dukes E, Kainu K, Suomela S,
Lappalainen M, Ziberna F, Korponay-Szabo IR, Kurppa K,
Kaukinen K, et al. (2009) IL23R in the Swedish, Finnish,
Hungarian and Italian populations: association with IBD and psoriasis, and linkage to celiac disease. BMC Med. Genet. 10: 8.
Elson CO, Cong Y, Weaver CT, Schoeb TR, McClanahan TK, Fick
RB, Kastelein RA. (2007) Monoclonal anti-interleukin 23 reverses active colitis in a T cell-mediated model in mice. Gastroenterology 132: 2359-2370.
Fedorak RN and Dieleman LA. (2008) Probiotics in the treatment
of human inflammatory bowel diseases. J. Clin. Gastroenterol.
Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, et
al. (2008) Defining the role of the MHC in autoimmunity: a review and pooled analysis. PloS Genet. 4:e1000024
Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S,
et al. (2008) Genetic determinants of ulcerative colitis include
the ECM1 locus and five loci implicated in Crohn’s disease. Nat.
Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL,
Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, et al (2010)
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat. Gen. 42:1118-25.
Fransen K, Visschedijk M, Sommeren S, Fu J, Franke L, Festen E,
Stokkers P, Bodegrave A, Crusius V, Hommes D, et al. (2010)
Analysis of SNPs with an effect on gene expression identifies
UBE2L3 and BCL3 as potential new risk genes for Crohn’s
disease. Hum. Mol. Genet. 19: 3482-3488.
Fritz T, Niederreiter L, Adoph T, Blumberg R, and Kaser A. (2011)
Crohn’s disease: NOD2, autophagy and ER stress converge. Gut.
Fujita N, Saitoh T, Kageyama S, Akira S, Noda T, and Yoshimori
T. (2009) Differential involvement of Atg16L1 in Crohn disease
and canonical autophagy: analysis of the organization of the
Atg16L1 complex in fibroblasts. J. Biol. Chem. 284: 32602-9.
Glas J, Seiderer J, Wetzke M, Konrad A, Török HP, Schmechel S,
Tonenchi L, Grassl C, Dambacher J, Pfennig S, et al. (2007)
rs1004819 is the main disease-associated IL23R variant in
German Crohn’s disease patients: combined analysis of IL23R,
CARD15, and OCTN1/2 variants. PLoS One 2: e819.
Glas J, Konrad A, Schmechel S, Dambacher J, Seiderer J, Schroff
F, Wetzke M, Roeske D, Török HP, Tonenchi L, et al. (2008)
The ATG16L1 gene variants rs2241879 and rs2241880 (T300A)
are strongly associated with susceptibility to Crohn’s disease in
the German population. Am J Gastroenterol 103: 682-91.
Hamm CM, Reimers MA, McCullough CK, Gorbe EB, Lu J, Gu
CC, Li E, Dieckgraefe BK, Gong Q, Stappenbeck, TS. (2010)
NOD2 status and human ileal gene expression. Inflamm. Bowel.
Dis. 16: 1649-57.
Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, et al. (2007)
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn’s disease in ATG16L1. Nat.
Genet. 39: 207-11.
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA,
Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, and
Wu GD (2009) High-fat diet determines the composition of the
murine gut microbiome independently of obesity. Gastroenterology 137: 1716-24.e1-2.
Hradsky O, Dusatkova P, Lenicek M, Bronsky J, Duricova D, Nevoral
J, Vitek L, Lukas M, and Cinek O. (2010) Two Independent
Genetic Factors Responsible for the Associations of the IBD5
Locus with Crohn’s Disease in the Czech Population. Inflamm.
Bowel. Dis. 1-7.
Hu C, Sun L, Hu Y, Lu D, Wang H, & Tang S. (2010) Functional
characterization of the NF-kappaB binding site in the human
NOD2 promoter. Cell. Mol. Immuno. 7: 288-95. Epub 2010 May
Hue S, Ahern P, Buonocore S, Kullberg MC, Cua DJ, McKenzie
BS, Powrie F, Maloy KJ (2006) Interleukin-23 drives innate and
T cell-mediated intestinal inflammation. J. Exp. Med. 203:
324 Genes & Genomics (2011) 33: 317-325
Hugot J, Chamaillard M, Zoual H, Lesage S, Cezard J, Belaiche J,
Almer S, Tysk C, O’Morain C, Gassull M, et al. (2001)
Association of NOD2 leucine rich repeat variants with susceptibility to Crohn’s Disease. Nature 411: 599-603.
Hugot J, Zouali H, and Lesage, S (2003) Lessons to be learned from
the NOD2 gene in Crohn’s Disease. Eur. J. Gastroenterol.
Hepatol. 15: 593-597.
Hugot J, Chamaillar, M, Zouali H, Lesage S, Cezard J, Belaiche J,
Almer S, Tysk C, O’Morain C, Gassull M, et al. (2009)
Association of NOD2 leucine rich repeat variants with susceptibility to Crohn’s Disease. Nature 411: 599-603.
Karlinger K, Györke T, Makö E, Mester A, Tarján Z (2000) The
epidemiology and the pathogenesis of inflammatory bowel
disease. Eur. J. Radiol. 35: 154-67.
Kim Y, Park J and Shaw M et al. (2008) The cytosolic sensors Nod1
and Nod2 are critical for bacterial recognition and host defense
after exposure to Toll-like receptor ligands, Immunity 28: 246-257.
Kobayashi T, Okamoto S, Hisamatsu T, Kamada N, Chinen H, Saito
R, Kitazume M, Nakazawa A, Sugita A, Koganei K, Isobe K,
and Hibi T. (2008) IL23 differentially regulates, the TH1/TH17
balance in ulcerative colitis and Crohn’s disease. Gut 57:
Kosovac K, Brenmoehl J, Hller E, Falk W, Schoelmerich J, Hausmann
M & Rogler G .(2010) Association of the NOD2 genotype with
bacterial translocation via altered cell-cell contacts in Crohn’s disease patients. Inflamm. Bowel. Dis. 16: 1311-21.
Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ (2008) Impaired
autophagy of an intracellular pathogen induced by a Crohn’s disease associated ATG16L1 variant. PLos ONE 3:e3391
Kullberg MC, Jankovic D, Feng CG, Hue S, Gorelick PL, McKenzie
BS, Cua DJ, Powrie F, Cheever AW, Maloy KJ, et al. (2006).
IL-23 plays a key role in Helicobacter hepaticus-induced T
cell-dependent colitis. J. Exp. Med. 203: 2485-2494.
Lacher M, Schroepf S, Helmbrecht J, von Schweinitz D, Ballauff A,
Koch I, Lohse P, Osterrieder S, Kappler R, Koletzko S (2010)
Association of the interleukin-23 receptor gene variant
rs11209026 with Crohn’s disease in German children. Acta.
Paediatr. 99: 727-33.
Lakatos P, Szamosi T, Szilvasi A, Molnar E, Lakatos L, Kovacs A,
Molnar T, Altorjay I, Papp M, Tulassay Z, et al. (2008) ATG16L1
and IL23 receptor (IL23R) genes are associated with disease susceptibility in Hungarian CD patients. Dig. Liver. Dis. 40:
Lecat A, Piette J, Legrand-Poels S (2010) The protein NOD2: an
innate receptor more complex than previously assumed. Biochem.
Pharmacol. 80: 2021-31.
Lee JC and Parkes M (2011) Genome-wide association studies and
Crohn’s disease. Brief. Funct. Genomics. 10: 71-6.
Levine,B (2005) Eating oneself and Univited Guests: Autophagy-Related Pathways in Cellular Defense. Cell 120: 159-162.
Loftus EV Jr. (2004) Clinical epidemiology of inflammatory bowel
disease: incidence, prevalence and environmental influences.
Lichtenstein GR, Hanauer SB, Sandborn WJ (2009) Practice Parameters Committee of the American college of gastroenterology.
Am. J. Gastroenterol. 104: 465-483.
Matthew C (2008) New links to the pathogenesis of Crohn disease
provided by genome-wide association scans. Nat. Rev. Genet. 9:
Matzinger P (2002) The danger model: a renewed sense of self.
Science 296: 301-5.
Maynard CL and Weaver CT (2009) Intestinal effector T cells in
health and disease. Immunity 31: 389-400.
McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette
P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH et al. (2008)
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nat. Gen. 40:
McGovern D, Rotter J, Mei L, Haritunians, T, Landers C, Derkowski
C, Dutridge D, Dubinsky M, Ippoliti A, Vasiliauska, E et al.
(2009) Genetic Epitasis of IL23/IL17 Pathway Genes in Crohn’s
Disease. Inflamm. Bowel. Dis. 15: 883-889.
Mitozugchi A and Mizoguchi E (2010) Animal Models of IBD:
Linkage to human disease. Curr. Opin. Pharmacol. 10: 578-587.
Mizoguchi A, Ogawa A, Takedatsu H, Sugimoto K, Shimomura Y,
Shirane K, Nagahama K, Nagaishi T, Mizoguchi E, Blumberg
RS, et al. (2007) Dependence of intestinal granuloma formation
on unique myeloid DC-like cells. J. Clin. Invest. 117: 605-615.
Molodecky NA and Kaplan GG (2010) Environmental risk factors
for inflammatory bowel disease. Gastroenterol. Hepatol. (N Y)
Nell S, Suerbaum S and Josenhans C (2010). The impact of the microbiota on the pathogenesis of IBD. Nat. Rev. Microbiol. 8: 564-77.
Newman WG, Zhang Q, Liu X, Amos CI, and Siminovitch KA (2009)
Genetic variants in IL-23R and ATG16L1 independently predispose to increased susceptibility to Crohn’s disease in a Canadian
population. J. Clin. Gastroenterol. 43: 444-7.
Noble CL, Nimmo ER, Drummond H, et al. (2005). The contribution
of OCTN1/2 variants within the IBD5 locus to disease susceptibility and severity in Crohn’s disease. Gastroenterology 129:
Noguchi E, Homma Y, Kang X, Netea M, and Ma X .(2009) A CD
associated NOD2 mutation suppresses transcription of human
IL10 by inhibiting activity of the nuclear ribonucleoprotein
hnRNP-A1. Nat. Immunol. 10: 471-479.
Ogura Y, Bonen DK, Inohara N et al. (2001). A frameshift mutation
in NOD2 association with susceptibility to Crohn’s disease.
Nature 411: 599-603.
Palomino-Morales, RJ, Gomez-Garcia, M, Lopez-Nevot, MA,
Rodrigo, L, Nieto, A, Alizadeh, BZ, and Martin, J (2009)
Association of ATG16L1 and IRGM genes polymorphisms with
inflammatory bowel disease: a meta-analysis approach. Genes.
Immun. 10: 356-364.
Peltekova VD, Wintle RF, Rubin LA et al. (2004) Functional variants
of OCTN cation transporter genes are associated with Crohn
disease. Nat. Genet. 36: 471-475.
Podolsky DK (2002) Inflammatory bowel disease. N Engl J Med 347:
Ramsay RR (2000) The carnitine acyltransferases: modulators of acyl-CoA-dependent reactions. Biochem. Soc. Trans. 28: 182-186.
Reinhard C and Rioux J (2006) Role of the IBD5 Susceptibility Locus
in the Inflammatory Bowel Diseases. Inflamm. Bowel. Dis. 12:
Repnik K. and Potocniki U (2010) CTLA3 CT60 Single-Nucleotide
Polymorphism is Associated with Slovenian Inflammatory Bowel
Disease Patients and Regulates Expression of CTLA4 Isoforms.
DNA Cell Biol 00: 1-8.
Rioux JD, Silverberg MS, Daly MJ et al. (2000) Genomewide search
in Canadian families with inflammatory bowel disease reveals two
Genes & Genomics (2011) 33: 317-325 325
novel susceptibility loci. Am. J. Hum. Genet. 66: 1863- 1870.
Roediger W and Nance S (1986) Metabolic induction of experimental
ulcerative colitis by inhibition of fatty acid oxidation. Br. J. Exp.
Pathol. 67: 773-782.
Sabbah A, Chang TH, Harnack R, Frohlich V, Tominaga K, Dube
PH, Xiang Y, and Bose S (2009) Activation of innate immune
antiviral responses by Nod2. Nat. Immunol. 10: 1073-80.
Silverberg M, Duerr R, Brant S, Bromfield G, Datta L, Jani N, Kane
S, Rotter J, Schumm P, Steinhart H, et al. (2007) Refined genomic
localization and ethnic differences observed for the IBD5 association with Crohn’s disease. Eur. J. Hum. Genet. 15: 328-335.
Singh SB, Davis AS, Taylor GA, and Deretic V (2006) Human IRGM
induces autophagy to eliminate intracellular mycobacteria.
Science 313: 1438-41. Epub 2006 Aug 3.
Stappenbeck T, Rioux J, Mizoguchi A, Saitoh T, Huett A,
Darfeuille-Michaud A, Wileman T, Mizushim N, Carding S,
Akira S, et al. (2010) Crohn Disease: A current Perspective on
Genetics, Autophagy and Immunity. Autophagy 7: 1-20.
Swoger JM and Binion, DG (2010) Supportive therapy in IBD: what
additional diagnoses and conditions must be treated? Dig. Dis.
Taylor KD, Targan SR, Mei L, Ippoliti AF, McGovern D, Mengesha
E, King L, Rotter JI (2008) IL23R haplotypes provide a large
population attributable risk for Crohn’s disease. Inflamm. Bowel.
Dis. 14: 1185-91.
Tokuhiro S, Yamada R, Chang X, Suzuki A, Kochi Y, Sawada T,
Suzuki M, Nagasaki m, Ohtsuki M , Ono M et al. (2003) An
Intronic SNP in a RUNX1 binding site of SLC22A4, encoding
an organic cation transporter, is associated with rheumatoid
arthritis. Nat. Genet. 35: 341-8.
Travassos LH, Carneiro LA, Ramjeet M, Hussey S, Kim YG,
Magalhães JG, Yuan L, Soares F, Chea E, Le Bourhis L, et al.
(2010). Nod1 and Nod2 direct autophagy by recruiting ATG16L1
to the plasma membrane at the site of bacterial entry. Nat.
Immunol. 11: 55-62.
Tysk C, Lindberg E, Järnerot G, and Flodérus-Myrhed B (1988)
Ulcerative colitis and Crohn’s disease in an unselected population
of monozygotic and dizygotic twins; A study of heritability and
the influence of smoking. Gut 29: 990-6.
Uhlig HH, McKenzie BS, Hue S, Thompson C, Joyce-Shaikh B,
Stepankova R, Robinson N, Buonocore S, Tlaskalova- Hogenova
H, Cua DJ, Powrie F (2006) Differential activity of IL-12 and
IL-23 in mucosal and systemic innate immune pathology.
Immunity 25: 309-318.
van Heel DA, Fisher SA, Kirby A, Daly MJ, Rioux JD, et al. (2004)
Inflammatory bowel disease susceptibility loci defined by genome
scan meta-analysis of 1952 affected relative pairs. Hum. Mol.
Van Limbergen J, Russell RK, Nimmo ER, Drummond HE, Smith
L, Anderson NH, Davies G, Gillett PM, McGrogan P, Weaver
LT, et al. (2008) Autophagy gene ATG16L1 influences susceptibility and disease location but not childhood-onset in Crohn’s disease in Northern Europe. Inflamm. Bowel. Dis, 14: 338-46.
Van Limbergen, J, Wilson, D, and Satsangi, J (2009) The Genetics
of Crohn’s Disease. Annu. Rev. Genomics. Hum. Genet. 10;
Wang, K Zhang, H, Kugathasan, S, Annese, V, Bradfield, J, Russel,
R, Sleiman, P, Imielinski, M, Glessner, J, Hou, C, et al. (2009)
Diverse Genome-wide Association Studies Associate the
IL12/IL23 Pathway with Crohn Disease. Am. J. Hum.Genet. 84:
Xavier R and Podolsky DK (2005) Commensal flora: wolf in sheep’s
clothing. Gastroenterology 128: 1122-6.
Xavier RJ and Podolsky DK (2007). Unravelling the pathogenesis
of inflammatory bowel disease. Nature 448: 427-34.
Xavier R (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nat.
Gen. 4: 1107-1112.
Zenhzhirong C, Xiaoqin W, Minhu C, Mei L, Xiang G, Baili C, and
Pinjin H (2009) Contribution of rs11465788 in IL23R gene to
Crohn’s disease susceptibility and phenotype in Chinese
population. J.Genet 88: 191-196.