Inflammatory Bowel Disease∗

18 Inflammatory Bowel Disease* Reed E. Pyeritz Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States

The inflammatory bowel diseases (IBDs) consist principally of ulcerative colitis (UC; OMIM#191390) and Crohn disease (CD; OMIM#266600), two chronic idiopathic inflammatory diseases of the gastrointestinal tract. UC and CD are considered together because of their overlapping clinical, epidemiologic, and pathogenetic features and shared complications and therapies. CD and UC also present distinct clinical, genetic, and pathologic characteristics. These similarities and differences suggest that UC and CD may be part of a continuum of IBDs.

18.1 INTRODUCTION AND DISEASE DEFINITION The common symptoms in UC and CD are diarrhea, abdominal pain, fever, and weight loss. UC is a chronic inflammation of the colonic and rectal mucosa, characterized by relapses and remissions of rectal bleeding [1a]. Inflammation in UC typically begins in the rectum and extends proximally in a continuous pattern without skipping areas of the colon. Inflammation is superficial, involving the mucosal/submucosal layers (the inner lining of the gut). In contrast to UC, inflammation in CD may occur anywhere in the gastrointestinal tract, from the mouth to the anus, with both involved and normal segments (skipped) of the intestine observable histologically and endoscopically. The most common form * An updated revision of the chapter in Principles and Practice of Medical Genetics, 6th ed. by Kent D. Taylor, Huiying Yang and Jerome I Rotter.

of CD is ileocolitis, affecting both the small bowel and the colon [1b]. When only the small bowel is affected, CD is also known as regional ileitis. In contrast to the superficial inflammation in UC, inflammation in CD is transmural, involving all layers of the bowel wall, mucosa, submucosa, and muscular layer, and sometimes progresses through the bowel wall. The chronic transmural inflammatory nature of CD can result in granulomas, abscesses, fistulae, and perianal complications. There is no etiologic-specific treatment for either form of IBD although colectomy is a curative procedure for UC. Currently, therapy begins with supportive measures and anti-inflammatory agents (e.g., the sulfasalazines and corticosteroids), with the addition of immunosuppressive agents when severe disease does not respond. In our current era, IBD does not increase mortality by itself [65b]. Traditionally, the diagnosis of CD and of UC has been based on clinical, radiologic, endoscopic, and histologic findings, and disease-specific antibodies have been explored for diagnosis (reviewed in Table 18.1). Serum antibodies to neutrophils staining with a perinuclear pattern (abbreviated pANCA) and serum anti-Saccharomyces cerevisiae antibodies (ASCA) are specific for the IBDs and symptomatic patients with one of these serologic marker diagnoses UC or CD without further invasive testing although this is not yet general practice. However, because of their relatively low sensitivity, these markers cannot be used as screening tools. In the future, these and other serum antibodies may be useful for classifying individuals with indeterminate colitis. Other serum antibodies will be discussed later.

Emery and Rimoin’s Principles and Practice of Medical Genetics and Genomics. https://doi.org/10.1016/B978-0-12-812532-8.00018-5 Copyright © 2020 Elsevier Inc. All rights reserved.

485

486

SECTION 3 

Gastrointestinal Disorders

TABLE 18.1  Diagnostic Criteria and Clinical Characteristics of Ulcerative Colitis (UC) and

Crohn Disease (CD) Method

Ulcerative Colitis

Anatomic location

Colon and rectum only

Radiologic

Endoscopic

Histologic

Extraintestinal

Subgroupings

Crohn Disease

Any part of the alimentary tract with the most common form ileocolitis Continuous distribution, fine granularity, Discontinuous and segmented distribution, deep fine superficial ulceration, fissures absent, ulceration extending into submucosa (transstrictures or fistulae rare fissures common, mural), thickening of mucosal folds, luminal strictures or fistulae common narrowing Disease almost always involves the rectum Rectum often spared, asymmetric and skip areas and extends proximally for varying disof inflammation, longitudinal ulceration, ileocecal tances, inflammation diffuse and continuinvolvement discrete ulcers in normal mucosa, ous, ulceration in inflamed mucosa, normal fissures, sinus, and fistulous ileocecal valve, tracts, abscesses, strictures, “cobblestone” appearance Disease principally involves mucosa; mucosa Disease is transmural, granulomas, fissures, irregularity, ulceration, increased chronic serositis, and fistulae, granulomas are key, but inflammatory cells in lamina propria. Goblet detectable in only 3%–50% of CD cases cell mucin depletion, and glandular disarray Common extraintestinal manifestations Frequency (24%) and type of common CD are include skin manifestations: Lesions, similar as those in UC, thrombotic and thromboarthropathies, ophthalmologic problems embolic vascular complications may occur in CD [66], disorders in hepatobiliary diseases occur in 21% of UC patients Proctitis, left-sided colitis, pancolitis Based on anatomic location: ileocolonic, ileitis, jejunoileitis, colonic CD. Based on nature of disease: perforating, nonperforating

Sands BE. From symptom to diagnosis: clinical distinctions among various forms of intestinal inflammation. Gastroenterology 2004;126:1518–32; Lashner BA. Clinical features, laboratory findings, and course of Crohn’s disease. In: Kirsner JB, editor. Inflammatory bowel disease. Saunders: Philadelphia; 2000. p. 305–14; Rankin GB. Extraintestinal and systemic manifestations of inflammatory bowel disease. Med Clin N Am 1990;74:39–50; Loftus Jr EV. Management of extraintestinal manifestations and other complications of inflammatory bowel disease. Curr Gastroenterol Rep 2004;65:506–13; Hommes DW, van Deventer SJ. Endoscopy in inflammatory bowel diseases. Gastroenterology 2004;126:1561–73; Farrokhyar F, Swarbrick ET, Grace RH, et al. Low mortality in ulcerative colitis and Crohn’s disease in three regional centers in England. Am J Gastroenterol 2001;96:501–7. Orchard T. Extraintestinal complications of inflammatory bowel disease. Curr Gastroenterol Rep 2003;55:512–7; Hoffmann RM, Kruis W. Rare extraintestinal manifestations of inflammatory bowel disease. Inflamm Bowel Dis 2004;10:140–7; Hofmeister A, Neibergs HL, Pokorny RM, Galandiuk S. The natural resistance-associated macrophage protein gene is associated with Crohn’s disease. Surgery 1997;122:173–8, discussion 178–9; Mintz R, Feller ER, Bahr RL, Shah SA. Ocular manifestations of inflammatory bowel disease. Inflamm Bowel Dis 2004;10:135–9.

The main reason for lack of specific treatments for these diseases is our continued poor understanding of the etiology and pathogenesis of the various forms of IBD. On the basis of the current evidence, exogenous or infectious agents, including variation in gut microflora, damage mediated by the immune system, and underlying genetic factors, combine to increase susceptibility to disease. Thus, genetic studies are essential for delineating etiologies underlying the continuum of the various forms of IBD. Understanding these etiologies promises

to point to cellular and immune pathways that will allow the subsequent development of radically new and specific therapies for these disorders. This understanding will also eventually target those at high risk for disease prevention. The remainder of this chapter reviews the supporting evidence for the genetic predisposition to various clinical groups of IBD and the progress in gene identification. This evidence includes ethnic differences in disease frequency, familial aggregation, an increased

CHAPTER 18 

monozygotic (MZ) twin concordance rate compared with that in dizygotic (DZ) twins, the existence of genetic syndromes that feature IBD, loci for CD and UC identified by genome scan and fine mapping, and finally, associations between various forms of IBD and specific genetic markers. Quite clearly, understanding the genetic architecture of the IBDs will increasingly guide therapies and reduce morbidity [2a,b,c]. 

18.2 PHENOTYPIC HETEROGENEITY Patients with UC or CD show great variability in their disease phenotypes for such characteristics as age of onset, rate of relapse, fibrostenosis, perforating/fistulizing, internal or perianal “penetrating disease” (fistulae, abscesses, or perforations), presence of diarrhea, bleeding or mucus discharge, duration of disease, location of disease (small bowel only, ileocolonic, colon only), number and types of surgery, development of chronic pouchitis after colectomy, and response to classes of medications such as corticosteroids, sulfasalazine or oral mesalamine, immunomodulatory agents (e.g., 6-mercapto-purine/azathioprine, methotrexate, cyclosporine), antibiotics, and topical therapies for distal colonic disease. Increasing evidence supports the clinical subgrouping of CD into perforating and nonperforating forms. Perforating CD is the more aggressive form, has a higher reoperation rate, and often results in abscesses and/or free perforation and fistulae. In contrast, the nonperforating form follows a more indolent clinical course and is associated with obstruction and bleeding [3]. This clinical subgrouping is further supported by cytokine mRNA profiles [4] and genetic marker studies [5a]. Some patients can be clearly classified as having CD based on histologic criteria yet have the UC-like features of left-sided colitis, more continuous and more shallow inflammation on endoscopy, and response to topical therapy. These phenotypic differences may reflect underlying differences in immunologic processes. IL-1 beta and IL-1 receptor antagonist mRNAs are increased in resected intestinal tissue from patients with nonperforating CD (the more benign form of CD) when compared with perforating CD [4]. CCR9-positive lymphocytes and CCR9 expressed in thymus distinguish small bowel from colonic CD. CD patients from families with multiple cases tend to have an early age at onset and more extensive disease as compared with those

Inflammatory Bowel Disease

487

from families with no other cases. Within families with multiple affected cases of CD, common familial patterns have been observed in the disease aggressiveness, age of onset, and disease location [5b]. Such familial distribution of clinical features suggests that certain genetic or environmental factors shared by family members may determine the clinical course of the disease. Thus, it may be beneficial to study a clinically homogeneous group in order to understand the role of certain genetic or environmental factors. Serum expression of pANCA and ASCA reflect mucosal processes. For pANCA, B-cell clones taken from the mucosa of UC patients express pANCA, directly demonstrating pANCA in the intestinal mucosa. For ASCA, the specificity of the expression of antimannan antibodies, rather than antigliadin or antiovalbumin in CD patients, of antibodies to Saccharomyces and not to Candida and of the expression of ASCA in patients with CD, rather than with UC or other colitides, suggests that ASCA expression manifests a CD-related immune response rather than reflects a nonspecific intestinal insult resulting from the inflammation. The expression of pANCA or ASCA extends the observed variability in IBD phenotype and provides further evidence for distinct subgroups within UC and CD. Within UC, the presence of pANCA has been associated with more severe forms of UC (treatment-resistant and left-sided UC, and the development of pouchitis following an ileal pouch-anal anastomosis [IPAA]) procedure [6a]. Within CD, the presence of pANCA is associated with a more UC-like disease [6b]. The pANCA phenotype demonstrates heterogeneity within UC with family data [7], and this heterogeneity appears to have a genetic basis, as demonstrated by the use of HLA class II [8] and the intercellular adhesion molecule-1 molecular polymorphisms. High titers of ASCA in CD are associated with early age of disease onset as well as with both fibrostenosing and internal penetrating disease; in contrast, high ANCA levels are associated with a later age of onset and different disease location. Because increasing evidence points to the role of an aberrant innate immune response or T-cell response to enteric bacteria, characterization of the serum expression of these antibodies may give clues to the specific microbial antigens involved in IBD pathogenesis. Western blots demonstrated that pANCA monoclonal antibody reacts to an unidentified Bacteroides caccae

488

SECTION 3 

Gastrointestinal Disorders

antigen and to an Escherichia coli outer membrane porin (OmpC) [9]. Subtractive cloning, using tissue from CD patients taken from lesions and nearby uninvolved tissue, led to the identification of I2, a Pseudomonas aeruginosa sequence that acts as a potent superantigen for CD4+ T-cell response [10]. OmpC, I2, ASCA, and pANCA have all been shown to be expressed in the sera of CD patients with more severe disease, characterized by small bowel involvement, frequent disease progression, longer disease duration, and greater need for intestinal surgery, and expression of more than one antibody is associated with more severe disease [11]. Serum expression screening has been used to identify specific bacterial antigens that drive IBD in the C3H/ HeJBir mouse model of colitis. A lambda DNA expression library was first constructed from bacteria obtained from mouse ceca and then screened with sera from colitic mice. A large proportion of the positive clones from this study were sequences related to bacterial flagellin from Butyrivibrio, Roseburia, Thermotoga, and Clostridium species (27%). However, none of the sequences directly matched a flagellin already identified and in the GenBank database [12a]. The fact that bacterial flagellin is one of the ligands of the Toll-like receptor TLR5 supports the role of the innate immune system in the pathogenesis of IBD [12b]. The most reactive antigen, CBir1 flagellin, was also expressed in sera from human patients with CD independent of the expression of the others [12a]. These observations suggest that ASCA, pANCA, I2, OmpC, and CBir1 are serum markers for different mucosal inflammatory mechanisms that underlie distinct disease expression, and that genetic variation may underlie these mechanisms. Rather than a complete loss of tolerance to all microbial antigens, IBD is characterized by subsets of patients with different responses to specific microbial antigens [13]. Use of clinical (fistulizing, perforating, fibrostenotic) and subclinical (ANCA, ASCA) characteristics may be useful in subdividing patient populations into more etiologically homogeneous groups for genetic studies and thus be the means for unraveling the genetic heterogeneity of these diseases in the future. In addition to giving clues on the bacteria and the specific immune defects that lead to the pathogenesis of IBD, these antibodies hold future promise for diagnosis of subsets of IBD and thus for specific treatments (Table 18.2). 

18.3 RACIAL AND ETHNIC DIFFERENCES Because the etiology of IBD is unknown, descriptive epidemiology plays a critical role in indicating the potential importance of genetic and environmental factors. However, owing to the difficulty of conducting population-based epidemiologic studies for these diseases, estimates of incidence and prevalence, especially in nonwhite populations, are imprecise. With the available data, the following can be generalized [14]. Whites have a higher risk than nonwhite populations [15]. There seems to be a north-to-south gradient in both North America and Europe [16], and IBD appears to be less common in developing countries. In North America and Europe, the most rapid increase of IBD occurred from 1960 to 1980 [5,14]. For the white population in North America (Manitoba), the annual incidence rate of IBD (per 100,000) from 1989 to 1994 was 14.6 for CD and 14.3 for UC, and the prevalence (per 100,000) in 1994 was 198.5 for CD and 169.7 for UC [17]. For a similar period (1983–93), a somewhat lower incidence and prevalence was observed in Minnesota (incidence: 6.9 and 8.3 per 100,000 for CD and UC, respectively) [18]. IBD risk in Europe is similar to that in North America [19]. A careful epidemiologic study of northern France has demonstrated that the incidence of CD has continued to increase in this region, rising from 5.2 per 100,000 from 1988 to 1990 to 6.4 per 100,000 from 1997 to 1999, and the incidence of UC has decreased from 4.2 to 3.5 per 100,000 in the same time periods [20]. In the United States, the white population has the highest risk among all ethnic groups, then blacks, followed by Mexican-Americans, and Asians [20]. In the United States, blacks with CD have a higher incidence of associated arthritis and uveitis compared with whites, and Mexican-Americans with UC have a higher incidence of pANCA expression (100% for Mexican-Americans compared with 40% for blacks) [21]. Outside of North America and Europe, the incidence of CD has been increasing recently, for example, in Puerto Rico (from 0.49 to 2 per 100,000), Taiwan (from 0.85 to 2.4 per 100,000), and Hong Kong for both CD (from 0.3 to 1.0 per 100,000). These increases suggest that an increase in Westernization may cause an increase in CD incidence. Although the differences in IBD frequency among various ethnic groups can have both environmental and genetic explanations, important evidence for a genetic

CHAPTER 18 

Inflammatory Bowel Disease

489

TABLE 18.2  Subclinical Markers for Inflammatory Bowel Disease Disease

Marker Studied

Type of Relatives

Observation

Combined IBD

Autoantibodies to epithelial-cell-associated component (ECAC) antigens Antinuclear autoantibodies (ANAs)

Family members

ECAC-C observed in 69.7% CD patients, 55.7% relatives, and only 8.0% control subjects

Family members

ANA observed in 18% CD patients, 43% UC patients, 13% of relatives of CD patients, 24% of relatives of UC patients, 2% control subjects Goblet cell autoantibodies Family members Positive GABs in 39% UC, 30% CD, 21% first-de(GABs) gree relatives of UC, 19% first-degree relatives of CD, 3% infectious enterocolitis, 2% healthy control subjects C-reactive protein (CRP) High specificity to differentiate CD from other functional bowel disorders Higher levels associated with higher disease activity and need for colectomy Crohn disease C3 dysfunction Family members Greater C3 dysfunction in CD (38%) and relatives (18%) than in control subjects Intestinal permeability Family members and Increased in CD patients, conflicting results twins regarding relatives Obligate anaerobic fecal Family members The flora of CD patients contained more anaerobic flora gram-positive coccoid rods and more gram-negative rods than that of healthy subjects; during 5–7 years follow-up, three of nine children with CD with a CD floral pattern showed CD symptoms and one such child was diagnosed as CD. None of the 17 children with a normal flora showed CD symptoms Subclinical intestinal inflam- Family members Calprotectin in CD patients (47 mg/L) and relatives mation (fecal calprotectin) (11 mg/L) higher than controls (4 mg/L), but not spouses (4 mg/L) Anti-Saccharomyces cerevi- Family members and ASCA increased in CD patients as compared with siae antibodies (ASCA) twins control subjects ASCA positive in 50% CD, increased in healthy relatives Pancreatic autoantibodies Family members Positive pancreatic autoantibodies in 27% CD (144% type I, 13% type II), subtype showed familial cluster, 0.5% in first-degree relatives Ulcerative Antineutrophil cytoplasmic Family members and Specific for UC, increased in healthy relatives of colitis antibodies twins UC patients, occur in a subset of CD patients Colonic mucins Twins HCM species IV (mucin subtype) reduced in both UC and healthy co-twins as compared with control subjects Mucosal production of IgG Twins UC patients and their healthy MZ co-twins showed subclass a raised proportion of IgG1 (78%) as compared with control subjects (56%) IgA against gliadin Twins High IgA titers against gliadin in both UC patients and their healthy co-twins CD, Crohn disease; HCM, human colonic mucin; IgA, immunoglobulin A; IgG, immunoglobulin G; MZ, monozygotic; UC, ulcerative colitis.

490

SECTION 3 

Gastrointestinal Disorders

TABLE 18.3  Examples of Inflammatory Bowel Disease Incidence/Prevalence Rates (per

100,000) Among Jewish and Non-Jewish Populations by Area and Time Period Area

Disease

Period

Jews

Non-Jews

Ratioa

Baltimore, MD

IBD UC CD CD CD CD CD CD UC CD UC

1960–63 1960–63 1960–63

16.7 13.3 3.4 12. 24.0 10.0 2.8 309 143 30 89

5.4 3.4 1.7 5.4 6.0 3.0 0.8 143 76 3.2b 9.8b

3.1 3.9 2.0 2.3 4.0 3.3 3.5 2.2 1.9 9.4 9.1

New York Malmo, Sweden Stockholm, Sweden Western Cape, South Africa Edmonton, Canada Southern Israel

1965–73 1960–74 1970–74 1977–81 1977–81 1990

CD, Crohn disease; IBD, inflammatory bowel disease; UC, ulcerative colitis. aRatio of Jewish/Non-Jewish patients. bIsraeli Arab.

TABLE 18.4  Positive Family History of Inflammatory Bowel Disease in Ulcerative Colitis (UC)

and Crohn Disease (CD) Probands: An Example

DISEASE IN RELATIVES Disease in Probands

Number of Crohn

UC Crohn disease Total

269 258 527

aBoth bWith

Probanda

UC (%)

Disease (%)

Mixedb (%)

Total (%)

37 (13.8) 19 (7.4) 56 (10.6)

6 (2.2) 32 (12.4) 38 (7.2)

4 (1.5) 9 (3.5) 13 (2.5)

47 (17.5) 60 (23.3) 107 (20.3)

Jews and non-Jews have the same trend. several affected relatives, some affected with UC and some with CD.

component to IBD susceptibility is the consistently increased incidence/prevalence in the Ashkenazi Jewish population compared with other ethnic groups in the same geographic location. The fact that the Jewish and non-Jewish differences occur across different time periods as well as different geographic areas [22] strongly suggests the existence of a genetic predisposition as the most parsimonious explanation (Table 18.3). Further support for this hypothesis comes from studies of the historical origins of Jewish subgroups and their relation to IBD frequency [22]. 

18.4 FAMILIAL AGGREGATION More than a dozen studies have demonstrated that familial aggregation is clearly increased in IBD although the data fit no simple Mendelian pattern of inheritance. Several studies have shown that there is an approximate

10- to 30-fold increase in disease prevalence among siblings compared with the community-wide prevalence. In addition to an increase in UC in relatives of UC patients and in CD among the relatives of CD patients, both UC and CD may exist in the same families, with an increased frequency higher than the co-occurrence by chance alone, suggesting an etiological relationship between UC and CD (Table 18.4). These families may identify a specific subset of IBD (mixed IBD), which currently would be defined by family history. Positive family history is somewhat greater among CD patients than among UC patients, and the relatives of CD patients have a higher risk for IBD than those of UC patients [23]. This suggests that CD is, to some degree, more often familial than UC and that CD has a greater genetic component (Table 18.4). In that study, the age of relatives was also taken into account to estimate the lifetime risks for disease. The lifetime risks for the relatives

CHAPTER 18  TABLE 18.5  Empiric Risks for Inflammatory

Bowel Disease (IBD) in First-Degree Relatives of Patients With Inflammatory Bowel Disease (%) Sibling

Parents Offspring Total

Uncorrected empiric risks for relatives of IBD probands Jewish probands affected with Crohn disease 8.0 3.0 Ulcerative colitis 2.4 3.2

1.8 1.9

4.5 2.6

Non-Jewish probands affected with Crohn disease 3.0 3.7 0 Ulcerative colitis 0.4 0.9 2.3

2.7 0.9

Corrected empiric lifetime risks for relatives of IBD probandsa Jewish probands affected with Crohn disease 16.8 3.8 Ulcerative colitis 4.6 4.1

7.4 7.4

7.8 4.5

Non-Jewish probands affected with Crohn disease 7.0 4.8 0 Ulcerative colitis 0.9 1.2 11.0

5.2 1.6

aCorrected

for age of at-risk relatives, using age-specific incidence data.

of non-Jewish patients were consistently lower than the corresponding risks for relatives of Jewish patients from the same geographic area (Table 18.5). This has implications for the mode of inheritance of genetic susceptibility. The serum expressions of ANCA and ASCA are also observed to be familial traits. An increased frequency of ANCA expression occurs in the clinically healthy relatives of UC patients compared with environmental controls [7]. Second-degree relatives, who did not share the same household with the probands, had an increased prevalence of ANCAs, and the household controls were not at an increased risk for ANCA. These observations suggest that the familial aggregation of ANCAs is due to shared genetic factors among the family members, and not shared environmental factors. Furthermore, in these family studies, there was a significant difference in the frequency of ANCAs in the relatives of probands whose sera were ANCA(+) compared with the relatives of probands whose sera were ANCA(−). This concordant familial distribution indicates heterogeneity within

Inflammatory Bowel Disease

491

UC. Thus, ANCAs may be used as a marker of an underlying immunologic disturbance that is genetically determined. Serum ASCA expression is a quantitative trait that is also familial in both affected and unaffected relatives of CD patients using intraclass correlation analysis [24]. A high percentage of CD patients (approximately half) and affected family members (also approximately half but with a lower level of expression) are seropositive for antimannan antibodies, compared with the normal control population (3.7%). Seropositivity or seronegativity correlates among all affected relatives and this association is stronger in affected first-degree relatives. Intraclass correlation reveals less variation in ASCA levels within, rather than between families, and a significant familial aggregation. There is no significant correlation among marital pairs. These findings demonstrate that ASCA in family members affected and unaffected with CD is a familial trait for both affected and unaffected relatives. The lack of correlation in marital pairs suggests that this familial aggregation is due in part to a genetic factor or childhood environmental exposure. 

18.5 TWIN AND SPOUSE STUDIES Although it is possible for the familial aggregation described in the preceding section to be due to environmental factors alone, additional support for a major genetic component to IBD susceptibility is provided by increased MZ twin concordance rates, the rarity of IBD concordance in spouses, and the numerous instances of affected relatives completely separated geographically and temporally from other affected family members. Even though twin data must be interpreted with caution because concordant pairs are more likely to be reported than discordant pairs, several studies have shown an increased concordance rate of both CD and UC in MZ twins when compared with DZ twins. In order to circumvent this selection bias, population-based twin studies have also been conducted with the same higher concordance rate for MZ twins than that for DZ twins for both CD and UC [25]. The concordance rate for CD is also higher than for UC (for example, the Swedish population-based study observed an MZ twin concordance of 58% for CD and 18% for UC). The higher concordance rate in MZ twins than in DZ twins supports the hypotheses that genetic factors are an important component in the development of IBD and that genetic

492

SECTION 3 

Gastrointestinal Disorders

factors account for much of the familial aggregation. The observation that <100% of MZ twins are concordant indicates that there is reduced penetrance for the IBD genotype, presumably due to nongenetic factors. These nongenetic factors may be environmental or they may be due to the random stochastic variation, for example, in the development of the B cells and T cells of the immune system [26]. The observation that the risk to DZ twins is not higher than the risk to siblings argues that the environmental factors are population-wide in their effect. From the limited number of family studies investigating the risk in spouses, it seems that the incidence of reported spouse concordance does not appear to be increased over population risks and is dramatically less than the risk to siblings. This observation argues against any rapid-acting environmental agents; there are, however, case reports of husband–wife couples that both developed IBD after marriage [27]. Therefore, these genetic epidemiologic studies of differences in IBD in various populations, of familial aggregation, and of twins and spouses of the affected have contributed to the basic concept that there is a major genetic contribution to susceptibility to IBD or diseases. 

18.6 INFERENCES REGARDING MODE OF INHERITANCE Although there is a strong familial aggregation of IBD and a major genetic component contributes to such familiality, there is no one simple genetic model that can explain the mode of inheritance of this disorder. From the MZ twin data, these are diseases with reduced penetrance, that is, genetic susceptibility does not appear to be the only determinant of disease [28]. The fact that DZ twins have a risk similar to that of siblings suggest that it is macro- (over a wide area), not micro- (within an individual household) environmental factors that determine the risk to IBD [29]. CD and UC are clearly genetically related because they are (a) found together with increased frequency in families, (b) both increased in the Jewish population compared with the surrounding white population, and (c) distributed in the same countries of origin for US Ashkenazi Jewish patients with IBD. On the basis of the stronger family history of IBD and greater MZ twin concordance for CD, genetic determinants appear to play a more deterministic role in CD than in UC. This does

not mean that UC is any less genetic but may be more influenced by stochastic variation [30]. There is now evidence for the involvement of specific loci and genes. Genetically modified animal models suggest that different genes can cause the same clinical phenotype. Animal models also indicate the importance of gene and environmental interactions. These observations and their implications for the mode of inheritance are summarized in Table 18.6.

18.6.1 Simple Mendelian Model Segregation analysis of the aggregation of disease within families demonstrates that IBD is not inherited in any simple Mendelian mode of inheritance. Using a computerized genetic analytic technique termed complex segregation analysis, a recessive gene with incomplete penetrance was proposed for CD [31a], and an additive major gene or a dominant major gene was proposed for UC [31b]. However, the conclusion of a major gene effect from complex segregation analysis is not equivalent to the conclusion of a major gene with simple Mendelian inheritance. Although these analyses argue strongly against the multifactorial/polygenic model, they cannot distinguish between simple Mendelian models and models with several major genes interacting (also known as multilocus or oligogenic model), or models of genetic heterogeneity (i.e., several genetically distinct diseases with a similar phenotype). Nevertheless, keeping the genetic heterogeneity of IBD in mind, the possibility of simple Mendelian susceptibility may be true for a subset of IBD. If so, even though these forms are rarer, the collection of families showing Mendelian segregation and subsequent locus and then gene identification within these families may be fruitful in showing biochemical or immunologic pathways relevant to the non-Mendelian and more frequent forms of IBD. 

18.6.2 Multifactorial/Polygenic Model [31c] In order to explain familial aggregation that does not follow a Mendelian pattern of inheritance, the polygenic model proposes that many genes, each with a small contribution to the phenotype, together provide the susceptibility to disease when the individual crosses a certain threshold. This model is termed multifactorial when these many genes must also interact with environmental factors. A polygenic model has been proposed to explain the association between CD and UC and to

CHAPTER 18 

Inflammatory Bowel Disease

493

TABLE 18.6  Genetic Inferences Based on Evidence of Family Aggregation in Inflammatory

Bowel Disease (IBD) 1. 2.

3.

4. 5. 6. 7. 8.

9. 10. 11.

IBD exhibits familial aggregation (a) Monozygotic twin concordance > dizygotic twin concordance (b) No increase in spouses (a) Positive family history in CD > UC

Increased risk factors within families Genetic factors responsible for familial aggregation

CD is more genetic or more deterministic; UC may be more stochastic and thus more immunologic

(b) Twin concordance of CD > UC Both CD and UC occur in the same families Very few “mixed” MZ twin pairs Risks are much greater in families than in the population Familial risks in Jews > familial risks in non-Jews in neighboring area Non-Jewish families have proportionally more “mixed” IBD (CD and UC) than Jewish families Clinical features concordant in CD families Increased risks to offspring when both parents have IBD Dizygotic twin concordance = sibling risk

Some genetic aspects of CD and UC are shared Some genetic aspects of CD and UC are distinct Genetic susceptibility is not polygenic Genetic susceptibility is not simple Mendelian “Mixed IBD” is not a simple overlap, but possibly a different disease, thus evidence for genetic heterogeneity Genetic heterogeneity Limited number of disease genes Environmental factors are probably not microenvironmental but macroenvironmental

CD, Crohn disease; MZ, monozygotic; UC, ulcerative colitis.

explain why the relatives of people with CD are much more likely to have IBD than the relatives of people with UC. The features of this model are the following: (1) a single genotype, comprising 10 or 15 genes, makes individuals susceptible to IBD and (2) if a person has only a few of these genes, they are more susceptible to UC, whereas if they have most of these genes (a more complete genotype), they are more susceptible to CD. Relatives of those patients with most of the genes (CD patients) would also be more likely to have a larger number of IBD susceptibility genes than the relatives of patients with only a moderate number of the risk genes (UC patients). Thus, CD patients would be more likely to have relatives with UC, whereas UC patients would be more likely to have relatives with too few of the highrisk genes to have any form of IBD. However, the formal mathematical genetic analyses of large family data sets of both UC and CD have allowed the rejection of the polygenic model. Basically, the risk of relatives is too great to be explained by this model. In addition, genetically modified animal models (including knockouts) suggest that if one gene in the immunoregulatory pathway is sufficiently altered, it can lead to clinical disease; thus, multiple genes with equal but small effects may not be required. 

18.6.3 Multilocus (Oligogenic) Model There is increasing evidence that the genetic predisposition to a number of diseases is due to the interaction of two or more major genes, a form of inheritance termed two locus (if two major genes are involved), or multilocus or oligogenic (if more than two are involved) [32a]. This model is important for IBD for several reasons. First, it is etiologically attractive because it is able to explain the occurrence of more than one pathophysiologic defect in IBD patients. For example, in order to develop clinical CD, one may need both a permeability defect that leads to increased exposure of the body’s immune system to antigenic substances that ordinarily do not cross the gut mucosal barrier and a particular genetically determined immune response. An analogous hypothesis might include abnormal mucins and certain autoantibodies as the etiologic factors in UC. Second, the multilocus model is able to explain the disparity between IBD recurrence risk estimates and typical risk estimates for Mendelian disorders [32a]. Third, the multilocus model is able to explain the relationship of UC and CD in families. For example, one gene may be insufficient by itself to lead to clinical disease yet predisposes to both diseases, but clinical disease occurs only when a second more specific gene interacts with the first and leads to

494

SECTION 3 

Gastrointestinal Disorders

the specific disease, either UC or CD. Fourth and finally, the multilocus model makes genetic counseling and risk identification in relatives feasible once the first susceptibility locus is identified, as has been demonstrated for other autoimmune diseases (Section 18.10). In one intriguing study, the risk of IBD in offspring when both parents have IBD is (1) more than twice the empiric risk to offspring of couples when one parent has IBD, (2) similar to the empiric risk for identical twins, and (3) higher for CD than for UC. The risk to offspring was similar whether both, one, or neither parent had developed symptoms of IBD at the time of the conception. Furthermore, the concordance rates for the type of IBD (UC or CD) in these couples were similar whether both experienced the onset of IBD before marriage, one before and one after, or both after marriage. These observations suggest that genetic and not acquired factors are essential in the development of IBD and in the determination of the type of IBD, whether UC or CD. Furthermore, although strong environmental determinants limited to certain families could be an explanation, these data support the concepts of a limited number of genetically determined forms of IBD, of a limited number of IBD-predisposing genes, and of the multilocus/ oligogenic model for IBD susceptibility. If many different genes were required or if there were many different genetic forms of IBD, then genetic complementation would reduce the risk to offspring. However, if there are a limited number of such genes, then the offspring of two affected parents are more likely to be homozygous at the loci for such genes and consequently affected. The number of genomic regions thus far identified using genome screen methods and the identification of several candidate genes further support the multilocus/ oligogenic model [32b]. 

18.6.4 Genetic Heterogeneity Model The heterogeneity model proposes that IBD is not a single disease but rather several diseases with different etiologies but presenting the same clinical picture. Advantages of this model are that, first, the identification of clinical subgroups leads to understanding separate etiologies corresponding to each of the specific subtypes of IBD and, thus, unravels an otherwise bewildering array of phenotype/genotype relationships, and second, genetic heterogeneity leads to testable etiologic hypotheses. The following observations support the idea of the genetic heterogeneity of IBD. (1) IBD is phenotypically

heterogeneous with emerging evidence on clinical subtypes (see earlier). (2) IBD is a feature of several different genetic syndromes (see later). (3) Animal models engineered by targeted gene disruption (knockout mice) illustrate that there are many pathophysiologic pathways to the development of IBD [70]. (4) The different relative frequencies of mixed disease (CD and UC) in the same family in Jewish versus non-Jewish families argue that the mixed form may be a distinct subgroup. Genetic heterogeneity leads to the predictions that genetically determined physiologic abnormalities in the affected case are likely to be shared with their relatives and that these would be similar within the same clinical subgroup. In this way, further support for the genetic heterogeneity of IBD comes from (5) the genetic serum expression of pANCA or of ASCA which define clinical subtypes of disease and are also present in the unaffected members of the family of affected (see later) and (6) the association of specific genetic markers with clinical subtypes within CD and UC associations which also suggest heterogeneity within CD and within UC. Therefore, the available evidence support the concepts that IBD is a genetically heterogeneous group of disorders, with each subform an oligogenic disorder due primarily to the interaction of a limited number of genes, although there may be more minor contributions from modifying genes. 

18.7 ASSOCIATION OF INFLAMMATORY BOWEL DISEASE WITH RARE GENETIC SYNDROMES IBD is clearly associated with three well-defined genetic syndromes: Turner syndrome, Hermansky–Pudlak syndrome (HPS) (OMIM #203300), and glycogen storage disease type lb (GSDIb) (OMIM #232220, Chr 11q23). In addition, IBD has been less clearly associated with several immunodeficiency syndromes (Table 18.7).

18.7.1 Turner Syndrome Several reports of patients with Turner syndrome, that is, individuals who lack all or part of one X chromosome, leave little doubt that the incidence of IBD is many times higher than that seen in the general population. This association may be due to the abnormal state of a single X chromosome; IBD has also been linked to the X chromosome in genome scans [13]. Alternatively, patients with Turner syndrome are known to be at increased risk

CHAPTER 18  TABLE 18.7  Genetic Syndromes

Associated With Inflammatory Bowel Disease Turner syndrome Hermansky–Pudlak syndrome Glycogen storage disease type 1b Sickle cell disease Trisomy 9 Immunodeficiency disorders Secretory immunoglobulin deficiency Agammaglobulinemia/hypogammaglobulinemia Selective IgA deficiency Chediak–Higashi syndrome Complement 2 (C2) deficiency Hereditary angioedema Pachydermoperiostosis IgA, immunoglobulin A.

of several diseases thought to involve autoimmunity. It may not be too surprising that IBD, also a potential autoimmune disease, is increased in these patients. CD and UC have been reported in about equal numbers in patients with Turner syndrome. 

18.7.2 Hermansky–Pudlak Syndrome HPS is a tyrosinase-positive form of oculocutaneous albinism with a lysosomal storage defect leading to accumulation of ceroid lipofuscin and with a platelet aggregation defect leading to a bleeding diathesis. The pattern of inheritance is autosomal recessive; many genes have now been identified, showing genetic heterogeneity in this disorder and multiple mutations have been observed with different subphenotypes, showing locus heterogeneity. HPS1 is rare except in the Puerto Rican population (where it is the most common genetic disorder with an incidence of 1:1800) and an isolated village in the Swiss Alps. HPS1 (OMIM *203300, Chr 10q23.1) was identified by linkage and positional cloning of families from these populations and is the homolog of the mouse “pale ear” gene. Different mutations at the HPS1 locus have been shown to be associated with IBD. HPS2 (OMIM #608233, Chr 5q14.1) differs from the other forms of HPS in that patients are immune deficient and susceptible to infections. HPS2 mutations are located in the beta-3A subunit of the adaptor protein complex 3 (AP3); AP3 forms transport vesicles for sorting protein traffic to lysosomes, melanosomes, and

Inflammatory Bowel Disease

495

platelet granules (AP3B1, OMIM *603401). The identification of the altered protein in HPS2 is, therefore, consistent with the pathophysiology of HPS and focuses further investigation on protein trafficking pathways for this disorder. Alterations in protein trafficking have also been observed to affect NK T-cell development and antigen presentation because endocytosed microbes are delivered to lysosomes for binding to MHC and CD1 molecules. Proteins HPS1 and HPS4 (OMIM *606682, Chr 22q11.2-12.2) form a complex that is involved in the biogenesis of lysosome-related organelles (BLOC-3, biogenesis of lysosome-related organelles complex 3). The role of HPS2 in cellular trafficking suggests that BLOC-3 is involved in a perhaps earlier step in sorting of proteins to organelles. HPS3 (OMIM *606118, Chr 3q24; syntenic with murine coat), HPS5 (OMIM *607521, Chr 11p15-p13), and HPS6 (OMIM *607522, Chr 10q24.32) form complex BLOC-2 and HPS3 is involved in the early stages of melanosome biogenesis and maturation. Interstitial pulmonary fibrosis with pulmonary insufficiency has been reported as the most frequent and serious complication of HPS1. In addition, a form of granulomatous colitis was reported in 5/9 HPS1 albinos in two Puerto Rican families living in New York and in 12/37 patients living in Puerto Rico [15]. HPS and granulomatous colitis are rare in non-Puerto Ricans. The clinical diagnosis in these colitis patients was UC, but the resected colons showed long linear ulcerations and microscopically focal mucosal non-necrotizing granulomas similar to CD but with variable amounts of brown granular pigment. In general, colitis has been refractory to medical treatment and appears to require surgical resection. No defect in peripheral blood lymphocyte or neutrophil function was identified. 

18.7.3 Glycogen Storage Disease Type Ib GSDIb (OMIM #232220) is an inherited metabolic disorder caused by a defect in the glucose-6-phosphate transporter (G6PT1; OMIM #602671). GSDIb contrasts with GSDIa (OMIM +232200), caused by a deficiency in the glucose-6-phosphatase (G6Pase). GSDIb is distinguished clinically from classic GSDIa by a predisposition to recurrent infections due to neutropenia and neutrophil dysfunction. In a study of 36 GSDIb patients from North America, 75% of subjects had some gastrointestinal symptoms and 28% had documented CD, and an additional 22% had symptoms

496

SECTION 3 

Gastrointestinal Disorders

highly suggestive of CD but had not been diagnosed [33]. CD is, therefore, associated with GSDIb, implicating neutrophil abnormalities in the pathogenesis of IBD. Neutrophils in GSDIa also show increased apoptosis. Long-term treatment with colony-stimulating factors (CSF2, OMIM *1389600, alias granulocyte– macrophage colony-stimulating factor, GM-CSF, and CSF3, OMIM *138970, alias granulocyte colony-stimulating factor, G-CSF) normalizes neutrophil count. Treatment with CSFs heals oral and intestinal mucosal lesions from CD in GSD-lb [34]. CSF3 is also in trial for treatment of non-GSDIb CD as an alternative to immunosuppression [34]. 

18.7.4 Immunodeficiency Syndromes The role of neutrophils in CD pathogenesis is further supported by the observations of CD-like lesions in neutrophil or bone marrow stem cell disorders: chronic granulomatous disease, congenital neutropenia, autoimmune neutropenia, leukocyte adhesion deficiency, and myelodysplastic syndromes (Table 18.7). A very interesting observation is that gut inflammation disappeared after stem cell transplantation for myeloid leukemia and myelodysplastic syndrome; this alleviation of inflammation persisted after immunosuppression was discontinued [35]. 

18.8 ASSOCIATIONS WITH OTHER DISEASES The association of IBD with many immune-related disorders with unknown etiology is well documented; these disorders include ankylosing spondylitis, psoriasis, primary sclerosing cholangitis, and pouchitis. IBD may also be associated with autoimmune disease in general (Table 18.8). One explanation for the association of IBD with other diseases is that the genetic component is a generalized defect of the immune system, which then may predispose the patient to several different autoimmune diseases or conditions. This hypothesis is supported by (1) the increased frequency of classic organ-specific autoimmune disorders observed in a large series of UC patients (e.g., autoimmune thyroid disease, insulin-dependent diabetes, and systemic lupus erythematosus) but not in CD patients [36]; (2) the concurrence of UC and celiac disease; and (3) genome scans for several

TABLE 18.8  Inflammatory Bowel Disease

Associated With Other Disorders

Ankylosing spondylitis (OMIM #106300) Psoriasis (OMIM %177900) Primary sclerosing cholangitis (OMIM #260480) Pouchitis Multiple sclerosis (OMIM #126200; %612594; %612595; %612596; #614810)

autoimmune disorders has shown that susceptibility to many autoimmune diseases share genomic regions, suggesting common susceptibility genes. The hypothesis further suggests that the etiology of the complications of IBD affecting only a portion of IBD patients may also share this generalized autoimmune disorder. This would be an example of genetic pleiotropy, one gene altering many phenotypes. These complications of IBD include uveitis, erythema nodosum, pyoderma gangrenosum, hepatitis, pancreatitis, and cirrhosis. In a large family with members affected with different autoimmune disorders, including rheumatoid arthritis, systemic lupus erythematosus, psoriasis, and IBD, it appears that family members with the same disease tend to share the same major histocompatibility complex (MHC) HLA haplotypes. Variation of the MHC class I polypeptide-related sequence A gene (MICA; GeneID 4276), also located within the MHC, has been associated with UC and with peripheral arthropathy. These observations suggest that one set of genes may determine the general autoimmunity of a patient, whereas other genes govern the specific constellation of phenotypes. 

18.9 GENE AND ENVIRONMENTAL INTERACTIONS Family and twin studies and genetic linkage and association studies evidence that genetic factors play an essential role in the development of IBD. However, the following observations argue for an additional environmental contribution to human IBD: (1) disease incidence has exhibited temporal trends and is correlated with industrialization or “Westernization”; (2) there is much less than a 100% concordance rate in MZ twins; (3) different disease risks have been observed for the same ethnic group residing in different geographic

CHAPTER 18 

Inflammatory Bowel Disease

497

locations; and (4) mouse models of IBD have demonstrated that intestinal bacteria are necessary for disease development. Therefore, it is likely that both gene and environmental factors determine the risk of developing IBD, and IBD is, thus, a complex genetic trait. Although the relationship of environment to IBD is complex, epidemiologic studies have identified several environmental factors that increase susceptibility to IBD.

18.9.3 Appendectomy

18.9.1 Smoking

18.9.4 Intestinal Bacteria

Smoking appears to have a protective effect for UC, with UC patients less likely to be smokers (OR = 0.17). Smoking may reduce overall symptoms, the need for surgery, and pouchitis. In contrast, smoking is positively associated with CD. A large meta-analysis across seven studies showed that smoking is associated with a greater susceptibility to CD (pooled odds ratio [OR] = 2.0, 95% confidence interval [CI] 1.65–2.47, for current smokers; OR = 1.8, 95% CI 1.3–2.5 for previous smokers). CD smokers showed a higher recurrence of repeat surgery through a 10-year follow-up period, particularly for women (OR = 4.2 for women; OR = 1.5 in men) [37], and this risk of recurrence is reduced when CD patients stop smoking. 

The study of animal models of IBD has given clear evidence that gut bacteria are necessary for intestinal inflammation and that inflammation results from an aberrant activation of the immune system driven by the gut lumen bacteria [40]. Inflammation develops when these various animals are raised in normal and in pathogen-free (SPF) conditions and does not develop when the animals are raised in very strict germ-free (GF) conditions. For example, inflammation does not develop with the IL10 knockout (ko) and TCRalpha ko mouse models grown in GF conditions; recolonization with Bacteroides vulgatus induces inflammation in both models and Helicobacter hepaticus alone induces inflammation in the IL10−/− (IL10 knockout) model (these bacteria are murine pathogens). An H. hepaticus flagellar hook protein has been identified as one of the specific antigens that induces colitis in the IL10−/− model. These knockout models also demonstrate that variation in many different genes leads to intestinal inflammation and show the greatest promise for investigating the relationships between cytokine genes and intestinal bacteria as well as the steps that lead to an imbalance between TH1 and TH2 cells in the intestinal immune system [70]. Another mouse model is adoptive transfer: mice homozygous for the SCID mutation develop IBD when isolated CD4+ T cells from another donor strain expressing high levels of CD45RBhigh antigen on their surface are transferred. Intestinal bacteria in the recipient mouse are also required for intestinal inflammation. This adoptive transfer model has demonstrated that both intestinal inflammation promoting and inhibiting cells are present in the intestinal immune system, and shows the greatest promise in dissecting the events in T-cell differentiation that lead to inflammation, particularly the relationship between the intestinal immune system and the thymus [41]. In one rat transgenic model, the human HLA-B27

18.9.2 Westernization As noted above, IBD appears to rise as a country becomes “Westernized” or industrialized. For example, a negative correlation between infant mortality or household hygiene and the incidence of CD has been demonstrated [38]. Many crucial changes occur in food, housing, transport, leisure, and clothing during this process, so that identification of the important exposure may be impossible. One recent hypothesis is that cooling of food during distribution and home refrigerators accounts for the rise in CD and is based on the following observations: (1) increases in incidence parallel public acquisition of refrigerators in the United States, Sweden, United Kingdom, and Southern Europe; (2) pathogenic psychotropic bacteria exist that are capable of growth within refrigerators, particularly Yersinia enterocolitica; (3) CD lesions occur in regions of high lymphoid follicles, suggesting the role of specific infection; (4) CARD15 mutations affect phagocytic cell lines, including monocytes, targets of Yersinia infection. 

A meta-analysis of 17 case control studies describing 3600 cases and 4600 controls showed that appendectomy was associated with a 69% reduction in subsequent risk of developing UC. A large Australian study observed that appendectomy was associated with more extensive UC but with a reduction in the requirement for immunosuppression or colectomy for the treatment of colitis [39]. 

498

SECTION 3 

Gastrointestinal Disorders

and beta-2 microglobulin genes have been introduced to replace the rat ortholog. Animals develop multiorgan disease that resembles the human spondyloarthropathies that accompany IBD in some individuals, colitis, arthritis, orchitis, and psoriasiform changes of the skin and nails; both colitis and arthritis do not occur when B27 transgenic rats are raised under GF conditions, implicating the normal enteric bacterial flora as the source of the antigens driving these diseases. E. coli and Enterococcus spp. are correlated with the amount of inflammation. This model has clearly demonstrated the role of the MHC class I antigen presentation system and shows the greatest promise to elucidate how presentation induces both intestinal and extraintestinal inflammation. New and unexpected ways to treat IBD should emerge from the intensive study of all of these types of models. The human gut microbiome will clearly have relevance to all future studies of intestinal inflammation [71]. The studies examined thus far clearly indicate the role of both genetic and environmental factors in the etiology of IBD. Clearly identifying the specifics of these risk factors will depend on the relative distribution of the particular factor. For example, in Western societies, a common environment may have brought the majority of people to an equal footing in terms of good hygiene, better nutrition, and improved maternal and pediatric care. In this case, when the environmental factors are common to all within the society, those individuals with the IBD susceptibility genes will be more likely to develop the disease as compared with those who do not have such genes. In this case, identifying the IBD susceptibility genes is possible, whereas identifying the IBD susceptibility environmental factors will be difficult. In contrast, the situation in which the environmental factors are not so common, as in developing countries that are experiencing a rising incidence of IBD, offers a window of opportunity for finding the specific environmental factors that contribute to IBD. Finding the environmental factors will be easier as the IBD susceptibility genes are identified. Therefore, well-designed genetic epidemiologic studies in developing countries are warranted as the incidence of IBD increases; these studies will have benefit for North America in addition to that particular developing country. 

18.9.5 An Evolutionary Perspective One question that should be raised in the context of this broad discussion of the genetic and the environmental risk factors for IBD is, “Why are IBD susceptibility alleles so frequent in the population?” There are three theoretical possibilities. First, IBD susceptibility could be due to new mutations. However, IBD susceptibility alleles clearly cause clinical disease with major morbidity and even mortality. The mortality was certainly greater until modern supportive management became available. If new mutations were the explanation, the mutation rate would have to equal both the mortality rate and the decreased reproduction due to the disease. For new mutations to explain the IBD disease frequency in the modern world, the mutation rate clearly would have to be much greater than the estimated range of 1 in 100,000 to 1 in 1 million/gene locus that appears to be the mutation rate in humans. Second, IBD susceptibility alleles could be the result of the founder effect. The founder effect refers to the concept that a given gene appeared (presumably by mutation) in a small ancestral population (i.e., in a founder) and by random chance was transmitted to a large number of that founder’s offspring. This would establish the gene in relatively high frequency in the original small population and its subsequent ancestors [42]. Although this founder effect is a reasonable explanation for the high frequency of certain genes in certain ethnic groups, it is an inadequate explanation for a disease (or diseases) with as wide a distribution and as high a frequency as IBD. Third, IBD susceptibility alleles may convey a selective advantage, either now or under conditions in the past; IBD susceptibility alleles are frequent, even though deleterious (disease causing), because they also provide some compensating advantage to those individuals who have them. This advantage would allow those humans with the allele (or alleles) to survive under a particular selective pressure, and thus, the IBD susceptibility alleles would increase in frequency in the population. A balance would be achieved when the advantageous effect of the alleles matches the frequency and severity of the disease for which they predispose. Understanding how IBD susceptibility alleles provide a selective advantage would be useful for two reasons. One reason is that this understanding would contribute

CHAPTER 18 

to our general understanding of human evolution and history. The second reason is perhaps more important: understanding the selective advantage of IBD susceptibility alleles will provide knowledge of the underlying physiologic process at a very fundamental level that would promote gene identification, unraveling disease pathogenesis, and thus suggest entirely new therapeutic approaches. Could IBD susceptibility genes provide a selective advantage? Such speculation should be built on several basic observations. IBD is clearly genetic, common, and occurs in many different ethnic groups throughout the world. Therefore, a selective advantage is likely to account for its high frequency. IBD is clearly a complex genetic trait and is likely to encompass a spectrum of many diseases that present with similar characteristics. Therefore, there are many steps affecting many pathways in IBD pathogenesis that could contribute to any selective advantage, and the advantage could be related to other diseases or other pathways not directly related to aberrant intestinal inflammation. IBD has clearly increased dramatically in the developed world over the 20th century and is now appearing (or being recognized) with increasing frequency in the developing world. This indicates that some environmental factor or factors still operating in recent historical times could provide the selection pressure in the developing world. This further suggests that the incidence of IBD rises because the selective advantage is no longer acting against the selection pressure because the environmental selection pressure is disappearing. The DZ twin rate for IBD is no greater than the sibling recurrence risk, suggesting that the environmental factors for IBD susceptibility affect the entire population. That is, the environmental factors are probably ubiquitous, rather than varying dramatically in frequency between families within a population or over a short time period (the few years of childhood). IBD is clearly an inflammatory and immunologic disease of the gut, suggesting that environmental factors that provide the selection pressure may have operated in the gut. This hypothesis could provide a possible explanation for the relatively higher frequency of IBD in the Jewish population. IBD appears to be highest in frequency

Inflammatory Bowel Disease

499

in Ashkenazi Jews, suggesting that the selective factor or factors had their greatest influence after the Ashkenazi/Sephardic division, coinciding with the historical division of Europe and the Mediterranean between the Christian and Islamic kingdoms [22]. However, the greatest frequency of IBD is distributed in those Ashkenazi Jews whose origin is in middle Europe [43] and is similar to the distribution of Tay–Sachs gene carriers. Historically, countries in middle Europe imposed the greatest ghetto urbanization on Jews, perhaps leading to the greatest overcrowding and to the consequent greatest defects in sanitation. This situation eased when the Ashkenazi Jews were invited to settle in Eastern Europe with less pressure from ghetto urbanization, that is, Poland, Ukraine, and Russia. More individuals that are Tay–Sachs heterozygotes or IBD patients come from middle as opposed to Eastern Europe [44]. The lower frequency of IBD in Israel when compared with that of Western Europe or the United States could possibly result from the more developing nature of that society. Regardless, if the specific details of this hypothesis are correct, it will be important to determine, if indeed, a genetically hyper-responding mucosal immune system is responsible for the susceptibility to IBD. 

18.10 GENE IDENTIFICATION 18.10.1 Genome-wide Linkage Studies The epidemiologic evidence demonstrating a major genetic contribution to IBD susceptibility has resulted in several genome scans for IBD susceptibility loci examining linkage to CD, UC, or IBD combined. Specific genomic regions identified by the whole genome approach have been further tested by yet more laboratories in more targeted linkage studies. This international effort is noteworthy within the study of the genetics of complex diseases in that several susceptibility loci for IBD have been identified by more than one laboratory. Table 18.9 shows the major IBD susceptibility loci demonstrated by linkage studies. Consensus has been reached by an international consortium on IBD genetics (International IBD Genetics Consortium) that the genome-wide approach provides evidence for susceptibility loci for IBD on chromosome 16q12 (IBD1) and on chromosome 12 (IBD2). More than two dozen loci have been found. Given that there are multiple susceptibility loci for IBD, and UC share some loci in common and

500

SECTION 3 

Gastrointestinal Disorders

TABLE 18.9  Susceptibility Loci for Inflammatory Bowel Disease Locus

Chromosomal Position

OMIM Reference

Susceptibility Gene(s) Identified

Associated Disease

IBD1 IBD2 IBD3 IBD4 IBD5 IBD6 IBD7 IBD8 IBD9 IBD10 IBD11 IBD12 IBD13 IBD14 IBD15 IBD16 IBD17 IBD18 IBD19 IBD20 IBD21 IBD22 IBD23 IBD24 IBD25 IBD26 IBD27 IBD28 IBD29

16q12.1 12p13.2-q24.1 6p21.3 MHC 14q11-q12 5q31 19p13 1p36 16p12 3p26 2q33.1 7q22 3p21.3 7q21.12 7q32.1 10q21 9q23 1p31.3 5p13.1 5q33.1 10q23-q24 18p11 17q21.1 1q32.1 20q13 21q22.1 12q15 13q13.3 11q23.3 1q32.1

#266600 %601458 %604519 %606675 %606348 %606674 %605225 %606668 %608448 #611081 %191390 %612241 #612244 #612245 %612255 %612259 #612261 %612262 #612278 %612288 %612254 %612380 %612381 %612566 #612567 #612639 %612796 #613148 #618077

NOD2 IBD2 HLA-DRBI*0103 TNF IBD4 SLC22A4/SLC22A5 IBD6 IBD7 IBD8 IBD9 ATG16L1 IBD11 ?MST1 ABCB1 IRF5 IBD15 IBD16 IL23R IBD18 IBD19 ?DLG5 IBD21 ?ORMDL3 IBD23 IBD24 ?CDFB4 IBD26 IBD27 IBD28 INAVA

CD UC IBD CD CD IBD IBD CD IBD CD IBD IBD IBD IBD IBD IBD CD CD CD IBD CD IBD IBD IBD Early IBD (AR) IBD CD Early CD (AR) CD

AR, autosomal recessive; CD, Crohn disease; IBD, inflammatory bowel disease; UC, ulcerative colitis.

do not share other loci, it is likely that some of these loci interact, and different loci play different roles in the IBD susceptibility of different populations. 

18.10.2 Chromosome 16 (IBD1, OMIM #266600) The chromosome 16 locus was the first locus to be identified by the whole genome approach [45], was quickly confirmed [46], and currently has the strongest experimental support worldwide. A two-point LOD score of 2.04 was observed for marker D16S409 in an initial family panel with 25 sibling pairs affected with CD with no known cases of UC (CD-only families) and in a second panel of 53 IBD families [45]. This result was confirmed in an independent sample the same year with a

peak multipoint LOD score (MLS) of 2.1 at D16S411 [46]. After stratifying based on Jewish ethnicity, the MLS increased to 2.4 for the non-Jewish families and decreased to lack of evidence for linkage in the Jewish families. This suggested that the chromosome 16 region contained a susceptibility locus for CD that is important for the non-Jewish population. Fine-mapping to a 1-cM resolution has resulted in an MLS of Z = 2.81 (P = .0003) at D16S416–D16S3117. Linkage of this region was also observed in families with UC only (NPL = 2.02, P = .02 at D16S3120) but, surprisingly, not in families with both CD and UC subjects (mixed families). The many loci subsequently determined are detailed in Table 18.8. 

CHAPTER 18 

18.11 META-ANALYSIS ACROSS ALL GENOME SCANS The field of the genetics of IBD is one of the leading fields in the genetics of complex traits in that there has been replication of several genomic regions. Nevertheless, many of the loci identified have not been reproduced across studies. This is somewhat expected because (1) there are differences in sampling between the various centers conducting these studies worldwide; (2) reliable detection of linkage requires a sample size that is larger than the usual linkage study performed in IBD genetics (∼100 sib pairs) [47]; and (3) even larger sample sizes are required for confirmation of a linkage result by a second study. The effort of the International IBD Genetics Consortium to combine linkage studies and genotype large numbers of individuals with the same microsatellite markers has been one strategy to overcome these problems. Another strategy has been to combine data from many linkage studies. The genome search meta-analysis method (GMSA) divides the genome into 120 bins 30 cM in size and ranks the evidence of linkage for that bin in each genome scan [48]. When applied to the genome scans for IBD susceptibility loci, IBD3 emerges as the most significant locus for IBD and CD [49,50], showing that a locus may attain greater significance in a combined data analysis than is apparent in a single-genome scan. The GMSA of four genome scans ranked IBD1 next in importance for IBD, and IBD5 and IBD1 next for CD, and the GMSA of van Heel et  al. ranked IBD1 and IBD6 for CD. 

18.12 CANDIDATE GENE STUDIES (TABLE 18.10) In the candidate gene approach, genetic variants are tested based on a prior hypothesis regarding the role of that gene or gene product in the pathophysiology of the disease. Such a hypothesis may be based on evidence from clinical observation or physiologic studies of affected individuals (in  vivo studies), from studies of known disease-related processes (in  vitro studies), from animal models of disease (transgenic construction or targeted disruption), and from the effects of drugs or chemicals on disease in either humans or animals (pharmacogenetic studies). For IBD, possible candidates could be selected from genes involved in

Inflammatory Bowel Disease

501

TABLE 18.10  Candidate Gene Studies MHC Interleukin 1β (IL1BI) and interleukin 1 receptor antagonist (IL1RN) ATP-binding cassette, subfamily B, member 1 (ABCB1) Interferon gamma receptor subunit 1 (IFNGR1) Solute carrier family 11 (SLC11A1) NOTCH (NOTCH4) Tumor necrosis factor (TNF) CARD15/NOD2 (IBD1) ICAM1 (IBD6) SLC22A4/SLC222A5 (IBD5)

the regulation of the balance between TH1 and TH2 cells; the response of humans to gut flora, particularly the innate immune system; and the release of cytokines during the immunologic destruction and healing of the intestinal mucosa.

18.12.1 The Major Histocompatibility Complex (MHC; IBD3)

The MHC on chromosome 6p21.3 is the most important genomic region for innate and adaptive immunity, containing genes involved in the regulation of the immune system and in antigen processing and presentation.

18.12.1.1 The MHC Class II Region In general, the class II molecules are dimeric, with an α-chain and a β-chain that form a groove for presenting an extracellular antigenic peptide to CD4+ T cells. The three class II molecules are HLA-DP, HLA-DQ, and HLA-DR. In each case, the α- and β-chains are encoded by A and B genes, respectively. For HLA-DR, there is an invariant HLA-DRA gene and up to three distinct and highly polymorphic HLA-DRB genes. One of these HLA-DRB genes, HLA-DRB1, is present in all individuals and is the most polymorphic. The study of HLADRB1 alleles has been an important tool in the study of the role of class II genes in IBD. Serologic methods identify several HLA-DR types and subtypes, and were used in the older studies, whereas molecular methods reveal even more subtypes at the nucleotide level. A meta-analysis of 29 studies reporting HLA-DR or HLA-DQ frequencies in CD and UC patients and in controls has been published [51]. 

502

SECTION 3 

Gastrointestinal Disorders

18.13 CLINICAL APPLICATION OF GENETIC INFORMATION Treatment of IBD was largely empiric (e.g., steroids and other anti-inflammatory drugs) until the advent of agents focused on specific mediators of pathogenesis. Clinical trials of novel drugs proceed at a rapid pace [52,53]. Genetic characterization of the IBD and the immune systems is emerging as useful in clinical practice. For example, for some years typing for ANCA and ASCA is helpful in diagnosing CD versus UC and in clarifying the cases of “indeterminate colitis.” As for the serum antibody markers pANCA and ASCA, they can be used in diagnosis. In the long term, genotyping patients for CD- and UC-associated genes will enable the determination of risk to relatives of IBD patients [54]. Similarly, genotyping will determine the optimal therapy for each individual [55]. Identifying the genes that predispose to each element of pathogenesis of IBD will point research into new directions to develop therapies and will enable the construction of mouse models for the testing of those therapies before starting clinical trials. The use of pharmacogenetic information already has a role in management [55]. Because glucocorticoids are known substrates for a drug efflux pump protein (P-glycoprotein 170) expressed by the MDR gene (SLC11A1, MDR1), the expression of this pump on the surface of lymphocytes was compared between IBD patients and controls, and increased MDR expression was observed in CD and UC patients who required surgery because they failed medical therapy. This observation suggests that a genetic variation that affects the pharmacology of steroids may lead to the ineffectiveness of these drugs in some IBD patients, and so the genetic contribution of SLC11A1 to IBD may be of interest to choosing proper therapies for individual patients. Clinical response to 6-mercaptopurine (6-MP) depends on its conversion to 6-thioguanine (6-TG) and reaching a TG level >235 (pmol/8 × 10−8 erythrocytes) [56]. Patients heterozygous for mutations that reduce the level of the enzyme thiopurine methyltransferase (TPMT) are able to attain this therapeutic level more readily on a given dose of 6-MP because the drug is not converted into inactive nucleotides by this enzyme (e.g., 6-methylmercaptopurine or 6-MMP). These results suggest that TPMT genotyping may assist the clinician in optimizing the therapeutic response to 6-MP and in identifying individuals at increased risk for drug-induced toxicity.

Patients in the original successful clinical trial of the anti-TNF antibody were also typed for ANCA status and genotyped in the TNF region of MHC [57]. The response of pANCA patients was the lowest and not significantly different from placebo, and the response of sANCA patients (a different type of staining from pANCA) was the highest in this study. Homozygotes for the LTA Ncol-TNFc-aa13L-aa26 haplotype “1-1-1-1” did not respond to treatment. Although these results must be interpreted with a great deal of caution because of the many comparisons made in this small study, these results raise the intriguing possibility that sANCA may identify a CD subgroup with a better response to Infliximab and that pANCA and homozygosity for the LTA “1-1-1-1” haplotype may identify CD subgroups with a poorer response [58]. Patients who do not respond favorably to TNF antagonists may also have diminished response to secondary agents [59]. Additional options for treatment continue to be developed [60] and hold the prospect for ongoing reduction of morbidity.Pharmacogenetics and pharmacogenomics will become increasingly important, with specific genetic markers, involved in either metabolism of the therapeutic agent or in the susceptibility to a form of IBD, increasingly guiding therapy [61]. Additionally, genetic screening will identify patients who are at particular risk of adverse effects of accepted therapies [62–64].

REFERENCES [1] (a) Sands BE. From symptom to diagnosis: clinical distinctions among various forms of intestinal inflammation. Gastroenterology 2004;126:1518–32.   (b) Lashner BA. Clinical features, laboratory findings, and course of Crohn’s disease. In: Kirsner JB, editor. Inflammatory bowel disease. Philadelphia: Saunders; 2000. p. 305–14. [2] (a) Batura V, Muise AM. Very early onset IBD: novel genetic aetiologies. Curr Opin Allergy Clin Immunol 2018;18:470–80.   (b) Liefferinckx C, Franchimont D. Viewpoint: toward the genetic architecture of disease severity in inflammatory bowel diseases. Inflamm Bowel Dis 2018;24: 1428–39.   (c) Marcin W, Michael S. Genetics and epigenetics of inflammatory bowel disease. Swiss Med Wkly 2018;148:w14671.

CHAPTER 18  [3] Greenstein AJ, Lachman P, Sachar DB, et al. Perforating and nonperforating indications for repeated operations in Crohn’s disease: evidence for two clinical forms. Gut 1988;29:588–92. [4] Gilberts EC, Greenstein AJ, Katsel P, et al. Molecular evidence for two forms of Crohn’s disease. Proc Natl Acad Sci USA 1994;91:12721–4. [5] (a) Helio T, Halme L, Lappalainen M, et al. CARD15/ NOD2 gene variants are associated with familially occurring and complicated forms of Crohn’s disease. Gut 2003;52:558–62.   (b) Loftus Jr EV. Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology 2004;126:1504–17. [6] (a) Sandborn WJ, Landers CJ, Tremaine WJ, Targan SR. Antineutrophil cytoplasmic antibody correlates with chronic pouchitis after ileal pouch-anal anastomosis. Am J Gastroenterol 1995;90:740–7.   (b) Vasiliauskas EA, Plevy SE, Landers CJ, et al. Perinuclear antineutrophil cytoplasmic antibodies in patients with Crohn’s disease define a clinical subgroup. Gastroenterology 1996;110:1810–9. [7] Shanahan F, Duerr RH, Rotter JI, et al. Neutrophil autoantibodies in ulcerative colitis: familial aggregation and genetic heterogeneity. Gastroenterology 1992;103:456–61. [8] Yang H, Rotter JI, Toyoda H, et al. Ulcerative colitis: a genetically heterogeneous disorder defined by genetic (HLA class II) and subclinical (antineutrophil cytoplasmic antibodies) markers. J Clin Investig 1993;92:1080–4. [9] Cohavy O, Bruckner D, Gordon LK, et al. Colonic bacteria express an ulcerative colitis pANCA-related protein epitope. Infect Immun 2000;68:1542–8. [10] Wei B, Huang T, Dalwadi H, et al. Pseudomonas fluorescens encodes the Crohn’s disease-associated I2 sequence and T-cell superantigen. Infect Immun 2002;70:6567–75. [11] Arnott ID, Landers CJ, Nimmo EJ, et al. Sero-reactivity to microbial components in Crohn’s disease is associated with disease severity and progression, but not NOD2/CARD15 genotype. Am J Gastroenterol 2004;99:2376–84. [12] (a) Lodes MJ, Cong Y, Elson CO, et al. Bacterial flagellin is a dominant antigen in Crohn’s disease. J Clin Investig 2004;113:1296–306.   (b) Takeda K, Kaisho T, Akira S. Toll-like receptors. Annu Rev Immunol 2003;21:335–76. [13] Vermeire S, Rutgeerts P. Antibody responses in Crohn’s disease. Gastroenterology 2004;126:601–4. [14] Loftus Jr EV. Management of extraintestinal manifestations and other complications of inflammatory bowel disease. Curr Gastroenterol Rep 2004;65:506–13.

Inflammatory Bowel Disease

503

[15] Probert CS, Jayanthi V, Hughes AO, et al. Prevalence and family risk of ulcerative colitis and Crohn’s disease: an epidemiological study among Europeans and South Asians in Leicestershire. Gut 1993;34:1547–51. [16] Shivananda S, Lennard-Jones J, Logan R, et al. Incidence of inflammatory bowel disease across Europe: is there a difference between north and South? Results of the European Collaborative Study on Inflammatory Bowel Disease (EC-IBD). Gut 1996;39:690–7. [17] Loftus Jr EV, Sandborn WJ. Epidemiology of inflammatory bowel disease. Gastroenterol Clin N Am 2002;31(1):1–20. [18] Bernstein CN, Blanchard JF, Rawsthorne P, Wajda A. Epidemiology of Crohn’s disease and ulcerative colitis in a Central Canadian Province: a population-based study. Am J Epidemiol 1999;149:916–24. [19] Palli D, Masala G, Trallori G, et al. A Capture–recapture estimate of inflammatory bowel disease prevalence: the florence population-based study. Ital J Gastroenterol Hepatol 1998;30:50–3. [20] Molinie F, Gower-Rousseau C, Yzet T, et al. Opposite evolution in incidence of Crohn’s disease and ulcerative colitis in northern France (1988–1999). Gut 2004;53:843–8. [21] Basu D, Lopez I, Kulkarni A, Sellin JH. Impact of race and ethnicity on inflammatory bowel disease. Am J Gastroenterol 2005;100:2254–61. [22] Rotter JI, Yang H, Shohat T. Genetic Complexities of inflammatory bowel disease and its distribution among the Jewish people. In: Bonne-Tamir B, Adam A, editors. Genetic diversity among Jews: diseases and markers at the DNA level. New York: OUP; 1992. p. 395–411. [23] Roth MP, Petersen GM, McElree C, et al. Geographic origins of Jewish patients with inflammatory bowel disease. Gastroenterology 1989;97:900–4. [24] Sutton CL, Yang H, Li Z, et al. Familial expression of anti-Saccharomyces cerevisiae mannan antibodies in affected and unaffected relatives of patients with Crohn’s disease. Gut 2000;46:58–63. [25] Halfvarson J, Bodin L, Tysk C, et al. Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. Gastroenterology 2003;124:1767–73. [26] Raulet DH, Vance RE, McMahon CW. Regulation of the natural killer cell receptor repertoire. Annu Rev Immunol 2001;19:291–330. [27] Comes MC, Gower-Rousseau C, Colombel JF, et al. Inflammatory bowel disease in married couples: 10 cases in Nord Pas de Calais region of France and Liege county of Belgium. Gut 1994;35:1316–8. [28] Ahmad T, Armuzzi A, Neville M, et al. The contribution of human leucocyte antigen complex genes to disease phenotype in ulcerative colitis. Tissue Antigens 2003;62:527–35.

504

SECTION 3 

Gastrointestinal Disorders

[29] Aldhous MC, Nimmo ER, Satsangi J. NOD2/CARD15 and the paneth cell: another piece in the genetic Jigsaw of inflammatory bowel disease. Gut 2003;52:1533–5. [30] Altmuller J, Palmer LJ, Fischer G, et al. Genomewide scans of complex human diseases: true linkage is hard to find. Am J Hum Genet 2001;69:936–50. [31] (a) Monsen U, Sorstad J, Hellers G, Johansson C. Extracolonic diagnoses in ulcerative colitis: an epidemiological study. Am J Gastroenterol 1990;857:711–6.   (b) Orholm M, Iselius L, Sorensen TI, et al. Investigation of inheritance of chronic inflammatory bowel disease by complex segregation analysis. BMJ 1993;306:20–4 (c) Fialkowski A, Beaslet TM, Tiwari HK. Multifactorial inheritance and complex diseases. In Principles and practice of medical genetics and genomics. 7th ed. Elsevier, London. pp. 323–358. [32] (a) Rotter JI, Landaw EM. Measuring the genetic contribution of a single locus to a multilocus disease. Clin Genet 1984;26:529–42.   (b) Juyal G, Sood A, Midha V, et al. Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018;97:1493–507. [33] Dieckgraefe BK, Korzenik JR. Treatment of active Crohn’s disease with recombinant human granulocyte-macrophage colony-stimulating factor. Lancet 2002;360:1478–80. [34] Melis D, Parenti G, Della Casa R, et al. Crohn’s-Like ileo-colitis in patients affected by glycogen storage disease Ib: two years’ follow-up of patients with a wide spectrum of gastrointestinal signs. Acta Paediatr 2003;92:1415–21. [35] D itschkowski M, Einsele H, Schwerdtfeger R, et al. Improvement of inflammatory bowel disease after allogeneic stem-cell transplantation. Transplantation 2003;75:1745–7. [36] Criswell LA, Pfeiffer KA, Lum RF, et al. Analysis of families in the multiple autoimmune disease genetics consortium (MADGC) collection: the PTPN22 620W allele associates with multiple autoimmune phenotypes. Am J Hum Genet 2005;76:561–71. [37] Sutherland LR, Ramcharan S, Bryant H, Fick G. Effect of cigarette smoking on recurrence in Crohn’s disease. Gastroenterol 1990;98:1123–8. [38] Montgomery SM, Pounder RE, Wakefield AJ. Infant mortality and the incidence of inflammatory bowel disease. Lancet 1997;349:472–3. [39] Florin TH, Pandeya N, Radford-Smith GL. Epidemiology of appendicectomy in primary sclerosing cholangitis and ulcerative colitis: its influence on the clinical behaviour of these diseases. Gut 2004;53:973–9. [40] Pierik M, Yang H, Barmada MM, et al. The IBD international genetics consortium provides further evidence

for linkage to IBD4 and shows gene–environment interaction. Inflamm Bowel Dis 2005;11:1–7. [41] Cheroutre H. Starting at the beginning: new perspectives on the biology of mucosal T cells. Annu Rev Immunol 2004;22:217–46. [42] Diamond JM, Rotter JI. Observing the founder effect in human evolution. Nature 1987;329:105–6. [43] Zlotogora J, Zimmerman J, Rachmilewitz D. Crohn’s disease in Ashkenazi Jews. Gastroenterology 1990;99:286–7. [44] Zlotogora J, Zimmerman J, Rachmilewitz D. Prevalence of inflammatory bowel disease in family members of Jewish Crohn’s disease patients in Israel. Dig Dis Sci 1991;36:471–5. [45] Hugot JP, Alberti C, Berrebi D, et al. Crohn’s disease: the Cold chain hypothesis. Lancet 2003;362:2012–5. [46] Ohmen JD, Yang HY, Yamamoto KK, et al. Susceptibility locus for inflammatory bowel disease on chromosome 16 has a role in Crohn’s disease, but not in ulcerative colitis. Hum Mol Genet 1996;5:1679–83. [47] Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science 1996;273:1516–7. [48] Pardi F, Levinson DF, Lewis CM. GSMA: software implementation of the genome search meta-analysis method. Bioinformatics 2005;21:4430–1. [49] Williams CN, Kocher K, Lander ES, et al. Using a genome-wide scan and meta-analysis to identify a novel IBD locus and confirm previously identified IBD loci. Inflamm Bowel Dis 2002;8:375–81. [50] Daly MJ, Pearce AV, Farwell L, et al. Association of DLG5 R30Q variant with inflammatory bowel disease. Eur J Hum Genet 2005;13:835–9. [51] Stokkers PC, Huibregtse Jr K, Leegwater AC, et al. Analysis of a positional candidate gene for inflammatory bowel disease: NRAMP2. Inflamm Bowel Dis 2000;6:92–8. [52] Danese S, Allez M, van Bodegraven AA, et al. Unmet medical needs in ulcerative colitis: an expert group consensus. Dig Dis 2019;6:1–18. [53] Pariente B, Hu S, Bettenworth D, et al. Treatments for Crohn’s disease-associated bowel damage: a systematic review. Clin Gastroenterol Hepatol 2018. pii: S1542355(18)10.1016. [54] Turpin W, Goethel A, Bedranki L, et al. Determinants of IBD heritability: genes, bugs and more. Inflamm Bowel Dis 2018;24:1133–48. [55] Lucafo M, Franca R, Selvestrel D, et al. Expert Opin Drug Metabol Toxicol 2018;14:1209–23. [56] Dubinsky MC, Lamothe S, Yang HY, et al. Pharmacogenomics and metabolite measurement for 6-mercaptopurine therapy in inflammatory bowel disease. Gastroenterology 2000;118:705–13.

CHAPTER 18  [57] Taylor KD, Plevy SE, Yang H, et al. ANCA pattern and LTA haplotype relationship to clinical responses to anti-TNF antibody treatment in Crohn’s disease. Gastroenterology 2001;120:1347–55. [58] Bazzoni F, Beutler B. The tumor necrosis factor ligand and receptor families. N Engl J Med 1996;334:1717–25. [59] Singh S, George J, Boland BS, et al. Primary non-response to tumor necrosis factor antagonists is associated with inferior response to second-line biologics in patients with inflammatory bowel diseases: a systemic review and meta-analysis. Dig Dis 2018;12:635–43. [60] Verstockt B, Ferrante M, Vermeire S, et al. New treatment options for inflammatory bowel diseases. J Gastroenterol 2018;53:585–90. [61] Venema WTU, Voskuil MD. Single-cell RNS sequencing of blood and ileal T cells from patients with Crohn’s disease reveals tissue-specific characteristics and drug targets. Gastroenterology 2019;156:812–5. [62] Panaccione R, Löfberg R, Rutgeerts P, et al. Efficacy and safety of adalimumab by disease duration: analysis of pooled data from Crohn’s disease studies. J Crohns Colitis 2019. https://doi.org/10.1093/ecco-jcc/jjy223. [63] Lucafò M, Franca R, Selvestrel D, et al. Pharmacogenetics of treatments for inflammatory bowel disease. Expert Opin Drug Metabol Toxicol 2018;14:1209–23. [64] Walker GJ, Harrison JW, Heap GA, et al. Association of genetic variant in NUDT15 with thiopurine-induced myelosuppression in patients with inflammatory bowel disease. J Am Med Assoc 2019;321:773–85. [65] (a) Hommes DW, van Deventer SJ. Endoscopy in inflammatory bowel diseases. Gastroenterology 2004;126:1561–73.   (b) Farrokhyar F, Swarbrick ET, Grace RH, et al. Low mortality in ulcerative colitis and Crohn’s disease in three regional centers in England. Am J Gastroenterol 2001;96:501–7. [66] Orchard T. Extraintestinal complications of inflammatory bowel disease. Curr Gastroenterol Rep 2003;55:512–7.

Inflammatory Bowel Disease

505

[67] Hoffmann RM, Kruis W. Rare extraintestinal manifestations of inflammatory bowel disease. Inflamm Bowel Dis 2004;10:140–7. [68] Hofmeister A, Neibergs HL, Pokorny RM, Galandiuk S. The natural resistance-associated macrophage protein gene is associated with Crohn’s disease. Surgery 1997;122:173–8. discussion 178–9. [69] Mintz R, Feller ER, Bahr RL, Shah SA. Ocular manifestations of inflammatory bowel disease. Inflamm Bowel Dis 2004;10:135–9. [70] Elson CO, Cong Y, Lorenz R, Weaver CT. New developments in experimental models of inflammatory bowel disease. Curr Opin Gastroenterol 2004;20:360–7. [71] Somienei HK, Kugathasan S. The microbiome in patients with inflammatory diseases. Clin Gastroenterol Hepatol 2019;17:243–55.

FURTHER READING Berntein CN, Forbes JD. Gut microbiome in inflammatory bowel disease and other chronic immune-mediated inflammatory diseases. Inflamm Intest Dis 2017;2:116–23. Hampe J, Hermann B, Bridger S, et al. The interferon-gamma gene as a positional and functional candidate gene for inflammatory bowel disease. Int J Colorectal Dis 1998;13:260–3. Orholm M, Fonager K, Sorensen HT. Risk of ulcerative colitis and Crohn’s disease among offspring of patients with chronic inflammatory bowel disease. Am J Gastroenterol 1999;94:3236–8. Rankin GB. Extraintestinal and systemic manifestations of inflammatory bowel disease. Med Clin N Am 1990;74:39–50. Yang H, Taylor KD, Rotter JI. Inflammatory bowel disease. In: King RA, Rotter JI, Motulsky AG, editors. The genetic basis of common diseases: oxford monographs on medical genetics. New York: Oxford University Press; 2002. p. 266–97. Yang H, Rotter JI. Genetic aspects of idiopathic inflammatory bowel disease. In: Kirsner JB, Shorter RG, editors. Inflammatory bowel disease. Baltimore: Williams & Wilkins; 1995.