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- •Foreword
- •Foreword
- •Contents
- •References
- •2.1 Introduction
- •2.2.1 Crohn’s Disease
- •2.2.2 Ulcerative Colitis
- •References
- •3.2.1 Bacterial Sensing
- •3.2.1.2 Toll-Like Receptors, TLRs
- •3.2.2 Autophagy: Autophagy-Related 16-like 1, ATG16L1
- •3.1 Introduction
- •3.2.4.1 Interleukin-23 Receptor, IL-23R
- •3.2.4.2 Fractalkine Receptor 1, CX3CR1
- •3.2.4.3 Transforming Growth Factor Beta (TGF-β)
- •3.2.4.4 Angiotensinogen
- •3.2.4.5 Tumour Necrosis Factor Alpha (TNFα)
- •3.2.6 Cell Signalling: Janus Kinase 2 (JAK2)
- •3.2.8 Other Processes
- •References
- •4.1 Introduction
- •4.2 Genetics
- •4.3 Epigenetics
- •4.5 DNA Methylation
- •4.9 MicroRNA
- •4.12 Summary
- •References
- •5.1 Introduction
- •5.2.1 TNFα
- •5.2.2 Th1 Cytokines
- •5.2.3 IL-1 Cytokines
- •5.2.4 Th2 Cytokines
- •5.2.5 Th17 Cytokines
- •5.2.6 TL1A
- •5.3 “Regulatory” Cytokines
- •5.3.1 TGFβ
- •5.3.2 IL-10
- •5.4 Concluding Remarks
- •References
- •6.1.1.1 Collagens
- •6.1.1.3 Glycoproteins
- •6.2.1 Integrins
- •6.3.1 Extracellular Matrix Stiffness
- •6.3.1.1 Modeling Extracellular Matrix Stiffness
- •References
- •7.1 Introduction
- •7.5 Future Outlook
- •References
- •8.1 Introduction
- •8.2.1 Smoking
- •8.3 Conclusion
- •References
- •9.4 Conclusions
- •References
- •10.1 Ulcerative Colitis
- •10.1.1 Epidemiology
- •10.1.2 Etiology
- •10.2.1 Pathogenesis
- •References
- •11.4 Conclusion
- •References
- •12.1 Introduction
- •12.2 Clinical Biomarkers
- •12.3 Cellular Biomarkers
- •12.4 Serologic Biomarkers
- •12.5 Other Factors
- •12.6 Conclusions
- •References
- •13.1 Introduction
- •13.3 Bowel Ultrasound
- •13.4 Computed Tomography Enterography
- •13.5 Magnetic Resonance Imaging
- •13.5.2 Functional MR Imaging Techniques
- •13.5.3 Hybrid Imaging Techniques
- •13.6 Conclusion
- •References
- •14.1.1 Ultrasound Stiffness Imaging
- •14.1.2 Shear Wave Elastography
- •14.5 Conclusion
- •References
- •15.1 Introduction
- •15.2.1 Stricturing IBD
- •15.2.2 Stricturing CD
- •15.2.3 Stricturing UC
- •15.4.1 Steroids
- •15.4.2 5-ASA
- •15.4.3 Purine Analogs
- •15.4.4 Methotrexate
- •15.4.5 Anti-TNFs
- •15.4.6 Other Biologics
- •15.5 Other Measures
- •15.6 Conclusion
- •References
- •16.1 Introduction
- •17.2.4 Abscess
- •17.3 Stricturoplasty or Resection
- •17.4 Approach
- •16.6 Conclusion
- •References
- •17.1 Introduction
- •17.2.2 Fibrotic Phenotype
- •17.2.3 Fistulising Disease
- •17.4.1 Open
- •17.4.2 Handassisted
- •17.4.3 Multi-Port
- •17.4.4 Single-Port
- •17.4.5 Single Port versus Multi-Port
- •17.4.6 Decision Making
- •17.5 Anastomosis
- •17.7 Conclusion
- •References
- •18.1 Introduction
- •18.4.1 Initial Evaluation
- •18.5.1 Pre-IPAA (Afferent Limb/Ileostomy Closure Site)
- •18.5.2 The Fibrotic IPAA Body
- •18.5.3 Post-IPAA (Efferent Limb, Anal Canal)
- •18.6 Conclusion
- •References
- •19.2 Pathophysiology
- •19.3 Diagnosis
- •19.4 Surgical Approach
- •19.4.1 Resections
- •19.4.2 Strictureplasties
- •19.4.2.1 History
- •19.4.2.2 Indications
- •19.4.2.3 General Technique
- •19.4.2.4 Conventional Strictureplasties
- •Judd Strictureplasty
- •Moskel-Walske-Neumayer Strictureplasty
- •Jaboulay Strictureplasty
- •Poggioli Strictureplasty
- •19.4.2.6 Results
- •Short-Term Results
- •Long-Term Results
- •19.5 Future Perspectives
- •References
- •20.1 Introduction
- •20.6 Summary
- •References
- •21.1 Introduction
- •21.2 Wound Healing
- •21.3 Crohn’s Disease Fistula
- •21.7 Summary
- •References
- •22.1 Introduction
- •22.3 The Transforming Growth Factor-β (TGF-β) Pathways
- •22.4.1 Connective Tissue Growth Factor (CTGF/CCN2)
- •22.4.2 Platelet Derived Growth Factor
- •22.4.3 Wnt-Signaling
- •22.4.4 Hedgehog Signaling
- •22.4.5 Notch Signaling
- •22.6.1 Coagulation Stage
- •22.6.3 Fibrous Adhesion Stage
- •22.7.4 Material Barriers
- •22.7.5 Pharmaceutical Approaches
- •22.8.4 Smooth Muscle Cells
- •22.12 Conclusions
- •References
- •23.1 Introduction
- •23.2 Liver
- •23.2.1 Farnesoid X Receptor (FXR)
- •23.2.2 Lysyl Oxidase (LOXL2)
- •23.2.3 Statins
- •23.2.4 5-Hydroxytryptamine (5HT)
- •23.2.5 Caspase Inhibition
- •23.2.6 Chemokine Receptors CCR2/5
- •23.2.7 GR-MD-02
- •23.2.8 PPAR Gamma
- •23.3 Lung
- •23.3.1 Pirfenidone
- •23.3.2 Nintedanib/Tyrosine Kinase Inhibitors
- •23.3.3 Lysophospholipids
- •23.3.4 mTOR
- •23.3.5 Prostacyclin
- •23.3.6 Integrin αvβ6
- •23.3.7 Endothelin Receptor Antagonism
- •23.3.8 Interleukin (IL)-13
- •23.3.9 Connective Tissue Growth Factor
- •23.3.10 Serum Amyloid P
- •23.4 Kidney
- •23.4.2 Pyridoxamine
- •23.4.3 Janus Kinase (JAK)1/2
- •23.4.4 Bindarit-CCL (MCP) Inhibitor
- •23.4.5 Phosphodiesterase Inhibition
- •23.5 Skin
- •23.5.1 TGFβ Targeted Therapies
- •23.5.2 Thalidomide/Pomalidomide
- •23.5.3 Paquinimod
- •23.6 Heart
- •23.6.1 Renin Angiotensin Aldosterone System (RAAS)
- •23.6.2 Transforming Growth Factor (TGF)-β
- •23.7 Conclusion
- •References
- •Index

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W. K. Ng and S. C. Ng

Chapter 3
Genetic Inuences ontheDevelopment
ofFibrosis inInammatory Bowel Disease
BramVerstockt, SareVerstockt, andIsabelleCleynen
Abstract Intestinal brosis is a common complication in inammatory bowel dis-
ease. These brotic processes develop in genetically susceptible individuals, inuenced by an interplay with environmental, immunological and disease-related
factors. A deeper understanding of the genetic factors driving brogenesis might
help to unravel the pathogenesis, and ultimately lead to development of new, antibrotic therapies. Here we review the genetic factors that have been associated with
the development of brosis in patients with both Crohn’s disease and ulcerative
colitis, as well as their potential pathophysiological mechanism(s).
Keywords Stricturing disease · Fibrosis · Crohn’s disease · IBD · Genetics ·
NOD2
3.1 Introduction
The study of the genetic architecture of inammatory bowel disease (IBD), with
Crohn’s disease (CD) and ulcerative colitis (UC) as its main entities, has made great
progress in the past decade. Genome-wide association studies and meta-analyses have
identied a total of 242 IBD risk loci [1]. Although many patients with CD or UC
undergo surgery during the course of their disease, with stricture formation being the
most common indication for major intestinal surgery—especially in CD, a genomic
basis that fully explains this disease heterogeneity has not yet been revealed [2, 3].
B. Verstockt
Translational Research in Gastrointestinal Disorders (TARGID), Department of Chronic
Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
Department of Gastroenterology and Hepatology, University Hospitals Leuven,
Leuven, Belgium
e-mail: bram.verstockt@kuleuven.be
S. Verstockt · I. Cleynen (
Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven,
Leuven, Belgium
e-mail: sare.verstockt@kuleuven.be; isabelle.cleynen@kuleuven.be
F. Rieder (ed.), Fibrostenotic Inammatory Bowel Disease,
https://doi.org/10.1007/978-3-319-90578-5_3
*)
13© Springer International Publishing AG, part of Springer Nature 2018

14
Bacterial
Cytokines
receptors
TEFβ
B. Verstockt et al.
The development of fibrosis in IBD is likely influenced by various genetic,
environmental, immunological and disease-related factors [4–7]. So far, the
relative contribution of each component in the pathogenesis is not clear. This
chapter aims to clarify the genetic contribution in developing fibrosis in patients
with IBD.
3.2 Genetics andFibrosis inCrohn’s Disease
Published literature on the genetic background of brotic CD is broad and very
often reports conicting data. Identied variants are involved in different biological
processes, suggesting that these processes contribute to the pathogenesis of brostenosis (Fig.3.1). Below we provide an overview of individual variants and genes that
have been associated with brotic disease in CD, and organized them according to
the biological process they are involved in (Table3.1). For each gene, we describe
its general function, list the variants associated with brotic CD, and how they could
be involved in the pathogenesis of brosis.
Bacterial sensing
Antigen
presentation
TLR
sensing
NOD2
NF-kB
ATG6L1
Autophagy
Fig. 3.1 Biological processes affected by the variants associated with brostenotic CD
Nucleus
cell
signaling
JAK
MHC
IL-23R
CXCRI
TNFα
and their

3 Genetic Inuences ontheDevelopment ofFibrosis inInammatory Bowel Disease
Reference
a
Sample
size
Caucasian 19,713 Cleynen etal. [26]
Studied
population
German 833 Glas etal. [27]
German 206 Brand etal. [28]
Caucasian 239 Sabate etal. [24]
Australian 235–112 Hume etal. [29]
Spanish 1090–1296 Alonso etal. [30]
15
(continued)
Discussed separately in
Table3.2
rs2066845, G908R
rs2066847, Leu1007fsinC
Gene or
region Polymorphism Association
b
Fibrostenotic disease
b,d
d
c
Fibrostenotic disease
Ileocolonic disease
IL-23R rs1004819 Ileal disease location
CX3CR1 rs3732379, V249I/rs3732378,
b
b
e
c
location
Fibrostenotic disease
rs3732379, V249I Fibrostenotic disease
T280M
TGF-β rs1800471, R25P Fibrostenotic disease
c
b
Fibrostenotic disease
Fibrostenotic disease
Bacterial sensing NOD2 rs2066844, R702W
Pathophysiological
process
Table 3.1 Key gene polymorphisms and their signicance in intestinal brosis in CD
Autophagy ATG16L1 rs2241880, T300A Ileal disease location Australian 669–154 Fowler etal. [25]
Antigen presentation MHC rs77005575 Disease behaviour
Cytokines and their
receptors
Epithelial barrier MAGI1 rs11924265 Fibrostenotic disease
Matrix metalloproteinases MMP-3 −1613 5T6T Colonic disease location Dutch 134 Meijer etal. [31]
Cell signalling JAK2 rs10758669 Ileal disease location Caucasian 1528 Cleynen etal. [17]

16
B. Verstockt et al.
Reference
a
Sample
size
Studied
population
c
[33]
Belgian 647 Forni etal. [32]
Belgian 875 Henckaerts etal.
Belgian 403 Holvoet etal. [34]
c
b
Gene or
region Polymorphism Association
Pathophysiological
process
Table 3.1 (continued)
rs1363670 Fibrostenotic disease
Close to
IL-12B
MIS18BP1 rs35223850 Fibrostenotic disease
Other processes FUT2 rs601338 Fibrostenotic disease
Adapted from Verstockt etal. Genetic Inuences on the Development of Fibrosis in Crohn’s Disease [3]
If a signicant association between the given variant and disease location is found in the reference, this is mentioned in the table
Not corrected for disease location
Number of included CD patients in primary cohort—number of included CD patients in replication cohort (if applicable)
a
Not signicant after Bonferroni-correction
Corrected for disease location
b
No longer signicant after multivariate analysis taking into account disease location
c
d
e

3 Genetic Inuences ontheDevelopment ofFibrosis inInammatory Bowel Disease
17
3.2.1 Bacterial Sensing
3.2.1.1 Nucleotide-Binding Oligomerization Domain-Containing Protein
2, NOD2
The NOD2 gene, located in the IBD1 locus on chromosome 16q12, is the most
studied gene in relation to brostenotic disease in CD. NOD2 encodes CARD15, a
member of the Apaf-1/NOD1 family of CARD (caspase recruitment domain containing protein) proteins [35, 36]. NOD2/CARD15 is mainly expressed by monocytes and macrophages, where it acts as a cytosolic sensor for bacterial products. It
is involved in apoptosis and activates NF-κB in response to lipopolysaccharide
(LPS), binding its leucine-rich repeating region (LRR) [11, 19]. Moreover, through
its CARD-domain, CARD15 is able to induce interleukin1-beta (IL-1β) processing
and release [37]. Importantly, NOD2 is also expressed in Paneth cells in the terminal
ileum [38].
In the early 2000’s, three NOD2 variants, including two amino acid substitutions
(R702W in exon 4, and G908R in exon 8) and one frameshift mutation (Leu1007fsinC
in exon 11), were found to be associated with CD susceptibility [16, 35, 39–41].
Several other NOD2 SNPs were later added to this list, although the rst three still
represent the strongest association signals. Many genotype-phenotype studies were
then performed to nd their role in dening specic CD subtypes (CD disease location and/or behaviour). While practically all studies agree on an association between
NOD2 and ileal disease location (Table 3.2), none of the NOD2 SNPs was uni-
formly found as an independent risk factor for developing brostenotic disease [6,
8–24, 26, 38, 42–55]. Some studies however did show associations between at least
one of the three NOD2 variants and brostenotic disease [19–21, 24], often independent of an association with small bowel disease [11, 14, 17, 22, 23] (Table3.2).
The lack of uniformity seems mainly based on the small sample sizes in the different studies (Table3.2). In a Northern-French population of 205 CD patients,
NOD2 R702W (rs2066844) was found a strong predictor of brostenotic disease,
independently of ileal disease location [8], but no other group could conrm this
association. An association of NOD2 G908R (rs2066845) and brostenotic disease
was rst reported in a Spanish CD cohort (n=204), although brostenotic disease
was mainly dependent on location of disease in the terminal ileum [9]. Later, a
meta-analysis including a total of 8833 CD patients reported G908R as being associated with brostenotic disease (pooled RR=1.90) [10]. It is important to highlight however, that only 12 of the included 49 studies in this meta-analysis had
enough data to analyse individual NOD2 variants, and most included studies did
not differentiate between G908R homo- and heterozygotes. Of the three NOD2
variants, the Leu1007fsinsC frameshift mutation (rs2066847) shows the strongest
association with brostenotic disease, but again it is unclear whether this is dependent on ileal disease involvement [11–14]. Seiderer etal. calculated a positive predictive value (PPV) of 80% and a negative predictive value (NPV) of 75% for the
diagnosis of small bowel stenosis in clinically symptomatic patients with a
Leu1007fsinC variant. Furthermore, they noticed 62% of their patients being

18
B. Verstockt et al.
Table 3.2 Overview of original studies showing an association between NOD2 and brotic CD
Polymorphism Association
rs2066844
Fibrostenotic Disease
Studied
population
a
French 205 Heresbach etal. [8]
Sample
size Reference
R702W
b
rs2066845
G908R
rs2066847
Leu1007fsinC
Fibrostenotic Disease
Fibrostenotic Disease
Ileal disease location North-American 201 Abreu etal. [11]
Fibrostenotic disease
Spanish 204 Mendoza etal. [9]
c
Meta-analysis 8833 Adler etal. [10]
c
Ileal disease location Italian 133 Vavassori etal. [12]
Fibrostenotic disease
b
Fibrostenotic DiseasebGerman 97 Radlmayer etal. [13]
Ileal disease location Italian 316 Annese etal. [14]
Fibrostenotic disease
c
Fibrostenotic DiseasebGerman 80 Seiderer etal. [15]
Ileal disease location German 303 Seiderer etal. [16]
Fibrostenotic disease
b
Ileal disease location Caucasian 1528 Cleynen etal. [17]
Fibrostenotic disease
a
Ileal disease location German 550 Schnitzler etal. [18]
b
d
All SNPs
combined
Fibrostenotic disease
Ileal disease location British 244 Ahmad etal. [19]
Fibrostenotic disease
Ileal disease location Finnish 271 Heliö etal. [20]
Fibrostenotic disease
b
Ileal disease location Hungarian 527 Lakatos etal. [21]
Fibrostenotic disease
b
Ileal disease location North-American 201 Abreu etal. [11]
Fibrostenotic Disease
a
Colonic disease location Caucasian 453 Lesage etal. [22]
Fibrostenotic Disease
a
Ileal disease location North-American 275 Brant etal. [23]
Fibrostenotic disease
a
Ileal disease location Italian 316 Annese etal. [14]
Fibrostenotic disease
a
Ileal disease location Caucasian 1528 Cleynen etal. [17]
Fibrostenotic disease
a
Ileal disease location Spanish 239 Sabate etal. [24]
Fibrostenotic disease
b
Adapted from Verstockt et al. Genetic Inuences on the Development of Fibrosis in Crohn’s
Disease [3]
If a signicant association between the given variant and disease location is found in the reference,
this is mentioned in the table
a
Corrected for disease location
b
Not corrected for disease location
c
Unclear if corrected for disease location
d
No longer signicant after multivariate analysis taking into account disease location

3 Genetic Inuences ontheDevelopment ofFibrosis inInammatory Bowel Disease
19
Leu1007fsinC homo- or heterozygous needed surgery, whereas the need for surgical intervention in patients without this variant was remarkably low [15]. A subanalysis of another cohort with 19 patients, all Leu1007fsinC homozygous,
identied a high-risk population, characterized by for instance long-segment stenosis, frequent need for surgery and high risk for re-stenosis afterwards [16]. The
same group conrmed these ndings later on in a prospective study [15], after
which the European IBDchip project reported comparable results in a retrospective
study (n=38) [17], as did Schnitzler etal. [18]. Besides studying the association
of individual NOD2 SNPs with a brostenotic CD phenotype, often the NOD2
SNPs are considered together. The pooled relative risk (RR) of stricturing disease
with the presence of any NOD2 variant allele was 1.33in the meta-analysis by
Adler etal. [10]. Furthermore, Lesage et al. clearly described the ‘gene dosage
effect’ of NOD2 SNPs: patients carrying two SNPs have a higher incidence of
stenosis compared to patients with one or two wild-type alleles [22], which was
afterwards conrmed by others [10, 23, 55]. There are also several studies that
could not nd an association between NOD2 variants and brostenotic disease:
Louis etal. found that only disease location and number of ares per year are signicantly different between different CD phenotypes, and that ileal disease location was associated with a stricturing disease pattern [51]. Although NOD2 variants
were associated with CD susceptibility in a Brazilian population, Baptista etal.
could not nd a genotype-phenotype correlation [43]. The biggest study thus far
looking into genotype-phenotype associations in IBD to date, also did not nd an
association between NOD2 and brotic disease, when considering disease location. They conclude that while disease location is in part genetically determined, it
is considered an intrinsic aspect of a patient’s clinical disease, and the major driver
to changes in disease behaviour over time [26]. Because of the strong correlation
between NOD2 variants and ileal disease location, we assume that the observed
association between brostenosis and NOD2 relies on a confounded association
due to disease location.
How could the NOD2 variants be pathophysiologically linked to the development of brosis? They might induce brostenotic disease by shifting T lymphocytes towards Transforming Growth Factor beta (TGF-β) cytokine production, and
by increasing collagen deposition by smooth muscle cells and broblasts in the
intestine [11]. Functional data are primarily available for Leu1007fsinC:
Leu1007fsinC leads to a truncated CARD15 protein, resulting in an altered activation of NF-κB following bacterial triggers [41]. It was previously thought that
Leu1007fsinC was associated with an impaired IL-1β production and dendritic
cell function, resulting in a dysregulation of the antibacterial host defence,
increased intestinal permeability and impaired regulation of innate and adaptive
immunity in the intestinal tract [15]. However, Maeda et al. later reported
Leu1007fsinC is associated with enhanced NF-κB activation and IL-1β secretion
in mice [37]. Additional mechanisms such as diminished mucosal alpha-defensin
expression might also be involved [15]. It is possible that the other two variants
also alter the structure of the LRR domain, resulting in abnormalities in bacterial
recognition [46].

20
B. Verstockt et al.
3.2.1.2 Toll-Like Receptors, TLRs
TLRs are transmembrane domain proteins with a tripartite structure: they contain an
extracellular domain (including LRRs) responsible for ligand recognition, a single
transmembrane spanning region, and a globular cytoplasmic Toll/IL-1 receptor
(TIR) signalling domain. Currently, ten TLRs are described in humans [56]. They
are expressed in myeloid cells and play a major role both in detecting microbes and
in initiating innate immune responses. TLR4, expressed in the Golgi apparatus of
intestinal epithelial cells, interacts with LPS, contributing to the perpetuation of
inammatory epithelial cell injury via Tumour Necrosis Factor Alpha (TNF-α)-
induced alterations of enterocyte turnover in an (auto)paracrine matter [21].
Rs4986790 (Asp299Gly) located within TLR4 has been shown to be a susceptibility variant for CD [57], although this could not be conrmed in another study by
Lakatos etal. (possibly because the variant allele is more present in their control
population compared to the study by Franchimont etal.) [21]. Neither of the two
studies found an association with CD sub-phenotype. This variant is associated with
decreased responsiveness to endotoxins in humans [58, 59]. Although there is no
genetic evidence for a role for TLR4 in the pathogenesis of brostenotic disease in
CD, Rieder etal. suggested the rst direct link between innate immunity to bacteria
(via TLRs) and brosis in humans [60]. Furthermore, in other diseases like systemic
sclerosis and liver brosis, TLR4 is thought to have a pathophysiological contribution [61, 62].
3.2.2 Autophagy: Autophagy-Related 16-like 1, ATG16L1
The ATG16L1 gene, member of a large family of genes involved in autophagocytosis, is located on chromosome 2q37. ATG16L1 is essential in the targeting and
destruction of pathogen-derived proteins in the innate immune response [63, 64].
Autophagy is also important for degrading cytoplasmic components, sequestered
within vesicles, by the lysosome [38].
The ATG16L1 T300A variant (rs2241880) is an important susceptibility variant
for CD [63, 65, 66]. This same variant has also been associated with ileal disease
location, independent of NOD2 genotype or disease duration; the study did not
mention an association with stricturing disease [64]. Later, Fowler etal. reported a
signicant association between brostenotic disease, the GG risk genotype and ileal
disease, independent of NOD2 (although the number of NOD2 variants in their
Australian CD population might be too small) [25]. However, the European IBDchip
Project could not conrm this association between ATG16L1 T300A and brostenotic disease [17].
The T300A amino acid substitution is a highly-conserved residue that is located
in the WD-repeat domain of ATG16L1, and may therefore affect interactions of the
protein with other components of the autophagosome [64]. This variant plays an
important role in pathogen clearance [67], resulting in imbalanced cytokine
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