Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Increased effectiveness of early therapy with anti-tumor necrosis factor-α vs an immunomodulator in children with Crohn's disease.

BACKGROUND & AIMS: Standard therapy for children newly diagnosed with Crohn's disease (CD) includes early administration of immunomodulators after initial treatment with corticosteroids. We compared the effectiveness of early (≤3 mo after diagnosis) treatment with an anti-tumor necrosis factor (TNF)α with that of an immunomodulator in attaining clinical remission and facilitating growth of pediatric patients. METHODS: We analyzed data from the RISK study, an observational research program that enrolled patients younger than age 17 diagnosed with inflammatory (nonpenetrating, nonstricturing) CD from 2008 through 2012 at 28 pediatric gastroenterology centers in North America. Patients were managed by physician dictate. From 552 children (median age, 11.8 y; 61% male; 63% with pediatric CD activity index scores >30; and median C-reactive protein level 5.6-fold the upper limit of normal), we used propensity score methodology to identify 68 triads of patients matched for baseline characteristics who were treated with early anti-TNFα therapy, early immunomodulator, or no early immunotherapy. We evaluated relationships among therapies, corticosteroid and surgery-free remission (pediatric CD activity index scores, ≤10), and growth at 1 year for 204 children. Treatment after 3 months was a covariate. RESULTS: Early treatment with anti-TNFα was superior to early treatment with an immunomodulator (85.3% vs 60.3% in remission; relative risk, 1.41; 95% confidence interval [CI], 1.14-1.75; P = .0017), whereas early immunomodulator therapy was no different than no early immunotherapy (60.3% vs 54.4% in remission; relative risk, 1.11; 95% CI, 0.83-1.48; P = .49) in achieving remission at 1 year. Accounting for therapy after 3 months, early treatment with anti-TNFα remained superior to early treatment with an immunomodulator (relative risk, 1.51; 95% CI, 1.20-1.89; P = .0004), whereas early immunomodulator therapy was no different than no early immunotherapy (relative risk, 1.00; 95% CI, 0.75-1.34; P = .99). The mean height z-score increased compared with baseline only in the early anti-TNFα group. CONCLUSIONS: In children newly diagnosed with comparably severe CD, early monotherapy with anti-TNFα produced better overall clinical and growth outcomes at 1 year than early monotherapy with an immunomodulator. Further data will be required to best identify children most likely to benefit from early treatment with anti-TNFα therapy.

Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study.

The etiology of growth impairment in Crohn's disease (CD) has been inadequately explained by nutritional, hormonal, and/or disease-related factors, suggesting that genetics may be an additional contributor. The aim of this cross-sectional study was to investigate genetic variants associated with linear growth in pediatric-onset CD. We genotyped 951 subjects (317 CD patient-parent trios) for 64 polymorphisms within 14 CD-susceptibility and 23 stature-associated loci. Patient height-for-age Z-score < -1.64 was used to dichotomize probands into growth-impaired and nongrowth-impaired groups. The transmission disequilibrium test (TDT) was used to study association to growth impairment. There was a significant association between growth impairment in CD (height-for-age Z-score < -1.64) and a stature-related polymorphism in the dymeclin gene DYM (rs8099594) (OR = 3.2, CI [1.57-6.51], p = 0.0007). In addition, there was nominal over-transmission of two CD-susceptibility alleles, 10q21.1 intergenic region (rs10761659) and ATG16L1 (rs10210302), in growth-impaired CD children (OR = 2.36, CI [1.26-4.41] p = 0.0056 and OR = 2.45, CI [1.22-4.95] p = 0.0094, respectively). Our data indicate that genetic influences due to stature-associated and possibly CD risk alleles may predispose CD patients to alterations in linear growth. This is the first report of a link between a stature-associated locus and growth impairment in CD.

Genetic determinants of pediatric inflammatory bowel disease: is age of onset genetically determined?

Inflammatory bowel disease (IBD) is thought to develop as a result of dysregulation of the immune response to normal gut flora in a genetically susceptible host. Approximately 25% of incident cases of IBD occur during childhood and the rest occur throughout adulthood, peaking in the second and third decades of life. What determines the age of onset remains unexplained currently. Studying early-onset presentation of complex diseases such as IBD is appealing to geneticists and scientists alike because of the expectation that these efforts will increase the probability of finding novel risk variants. Genome-wide association studies (GWAS) have yielded more susceptible loci in IBD than in any other complex common disease studied. Using 35 confirmed Crohn's disease risk alleles from adult studies, a recent pediatric replication study detected no significant association between risk score and age of onset through age 30, indicating age of onset does not have any impact on increased disease development in IBD. The first GWAS study using an exclusively pediatric IBD cohort found 2 novel risk variants that were not previously reported in predominately adult GWAS studies. However, during the data-mining of adult GWAS, these 2 novel loci (TNFRSF6 and PSMG1) were found with nominal significance suggesting that these risk loci are not restricted to early-onset CD cases. These analyses illustrate that the genetic effects of established CD risk variants is similar in early- and late-onset CD. However, the quest to find early-onset IBD risk variants is continuing. As such, GWAS studies involving large pediatric-onset CD cohorts and early-onset ulcerative colitis presentations are presently underway. A future joint analysis of genome-wide association data of early- and late-onset cohorts will likely reveal more IBD risk variants since the power to detect small effects of genes increases.

Male sex and intraventricular hemorrhage.

BACKGROUND: Neonatal mortality and morbidity are sex biased in low birth weight infants. The "Y chromosome effect" has been suggested to be responsible for these maturational differences. OBJECTIVE: To examine the association of sex and neonatal outcomes. DESIGN AND METHODS: A retrospective observational study. Data on all low birth weight infants who survived for >48 hrs were analyzed. Neonatal outcomes were compared between male and female infants. A regression model was used to detect the influence of sex on outcomes after controlling for confounders. Analysis was repeated after stratification of infants into three groups: group A (<1000 g), group B (1000-1499 g), and group C (1500-2499 g). RESULTS: A total of 833 infants were included in this study; 419 female infants and 414 male infants. Male infants had an increased rate of overall intraventricular hemorrhage (IVH) (12.2% vs. 7.2%, p = .02) and IVH grades 3-4 (4.8% vs. 2.3%, p = .04). In addition, male infants had higher bilirubin levels (10.19 +/- 3.1 mg/dL vs. 9.32 +/- 2.94 mg/dL, p = .001). In a regression model, male sex continued to have significant influence on IVH, IVH grades 3-4, death, and bilirubin. In group A, male infants had a significantly increased prevalence of death (regression coefficient, 1.82 +/- 0.65; p = .005) that could not be explained by the increased prevalence of IVH (p = .18) in regression analysis. In group B, male sex was significantly associated with a higher bilirubin level (regression coefficient, 0.94 + 0.3; p = .002). In bivariate analyses, IVH and IVH grades 3-4 were significantly higher in male compared with female infants (19.8% vs. 3.9%, p < .0001) and (8.5% vs. 0.97%, p = .02), respectively, but these differences lost significance in multiple-regression analysis. In group C, male sex positively influenced the prevalence of IVH (regression coefficient, 1.7 +/- 0.57; p = .003). Bilirubin measured higher in male infants (11.38 +/- 2.87 mg/dL vs. 10.19 +/- 3.22 mg/dL, p = .0004), but the difference lost significance in regression analysis (regression coefficient, 0.21 +/- 0.31; p = .5). CONCLUSIONS: Bilirubin, IVH, and death were significantly higher in male infants. In subgroup analysis, significance was retained in group A (<1000 g). Whether a single biological factor is responsible for these differences or perhaps a multi-causal process involving a complex interaction of physiologic, environmental, and pathologic responses needs to be further addressed in future research.

Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping.

BACKGROUND: The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. METHODS: We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn's disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn's disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. CONCLUSIONS: The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD.

Report of the CCFA pediatric bone, growth and muscle health workshop, New York City, November 11-12, 2011, with updates.

Growth retardation, delayed puberty, decreased bone mass, altered bone architecture, hypovitaminosis D and skeletal muscle mass deficits are common in children with inflammatory bowel diseases. The Crohn's and Colitis Foundation of America sponsored a multidisciplinary workshop on the subject of Bone and Skeletal Growth in Pediatric IBD, held in New York City in November 2011. The topic of the workshop was a key recommendation of the Foundation's Pediatric Challenges meeting in 2005. The Litwin Foundation provided a generous grant to support this crucial research and workshop through the CCFA. The workshop featured 15 presentations by researchers from the United States, Canada, Switzerland, Germany, and the United Kingdom and a number of posters elucidating diverse aspects of the problem of growth retardation and compromised bone health in pediatric Crohn's disease and ulcerative colitis. The workshop comprised original, basic, and clinical research and relevant reviews of underlying genetics, molecular biology, endocrinology, immunology, and bone physiology research. Investigators funded by CCFA and the Litwin Family Foundation are marked by an asterisk after their name in the text. Workshop presentations fell under 3 broad categories: "Mechanisms of Suppression and Growth of Bone Cell Function by Inflammation," "Impact of IBD on Growth and Bone Health," and "Approaches to Address Growth Failure and Low Bone Mass in Children with IBD," summarized herein. We have cited the publications that resulted from this granting mechanism in the appropriate section and references for pertinent updates on each topic.

Is mechanical ventilation associated with intraventricular hemorrhage in preterm infants?

BACKGROUND: The impact of mechanical ventilation on the incidence of intraventricular hemorrhage (IVH) in very low birth weight (VLBW) infants is unknown, simply because the vast majority of these infants have been routinely intubated and mechanically ventilated. There is a growing interest in the use of early nasal continuous positive airway pressure (ENCPAP) and avoiding mechanical ventilation. OBJECTIVES: To examine the role of mechanical ventilation since delivery room in determining severe IVH in VLBW infants in two neonatal units that follow the same strategy of respiratory management using ENCPAP. METHODS: We collected data on delivery room intubation and mechanical ventilation during the first 3 days of life in VLBW infants. Logistic regression model was constructed to test the relationship between early mechanical ventilation and the diagnosis of severe IVH after controlling for significant confounding variables, such as BW, gender, duration of mechanical ventilation, and partial pressure of CO(2) (PCO(2)). RESULTS: Of the studied 340 VLBW, 35 infants had severe IVH; most of them received mechanical ventilation that started either in the delivery room (n=12) or during the first (n=10) and second (n=3) days of life. Severe IVH was independently associated with lower BW, mechanical ventilation in the delivery room, and the cumulative duration of mechanical ventilation during the first 3 days. The adjusted odds ratio for severe IVH in infants intubated in delivery room was (OR=2.7, CI: 1.1-6.6, P=0.03). Severe IVH was not associated with gender, prenatal steroids, early sepsis, or patent ductus arteriosus. CONCLUSIONS: Mechanical ventilation plays a role in predicting severe IVH. Both the time at which ventilation was initiated and the duration of ventilation are important determinants of severe IVH. Risk for severe IVH in infants who were never intubated in delivery room or during the first 3 days of life is miniscule.

Genome-wide association identifies multiple ulcerative colitis susceptibility loci.

Ulcerative colitis is a chronic, relapsing inflammatory condition of the gastrointestinal tract with a complex genetic and environmental etiology. In an effort to identify genetic variation underlying ulcerative colitis risk, we present two distinct genome-wide association studies of ulcerative colitis and their joint analysis with a previously published scan, comprising, in aggregate, 2,693 individuals with ulcerative colitis and 6,791 control subjects. Fifty-nine SNPs from 14 independent loci attained an association significance of P < 10(-5). Seven of these loci exceeded genome-wide significance (P < 5 x 10(-8)). After testing an independent cohort of 2,009 cases of ulcerative colitis and 1,580 controls, we identified 13 loci that were significantly associated with ulcerative colitis (P < 5 x 10(-8)), including the immunoglobulin receptor gene FCGR2A, 5p15, 2p16 and ORMDL3 (orosomucoid1-like 3). We confirmed association with 14 previously identified ulcerative colitis susceptibility loci, and an analysis of acknowledged Crohn's disease loci showed that roughly half of the known Crohn's disease associations are shared with ulcerative colitis. These data implicate approximately 30 loci in ulcerative colitis, thereby providing insight into disease pathogenesis.

Early nasal continuous positive airway pressure and necrotizing enterocolitis in preterm infants.

BACKGROUND: The use of early nasal continuous positive airway pressure (ENCPAP) as the mode of initial respiratory support for very low birth weight (VLBW) infants has been increasing. The impact of CPAP and oxygen on gut mucosa and perfusion in premature infants is not known. The relation between ENCPAP and necrotizing enterocolitis (NEC) has not been adequately addressed. OBJECTIVE: To evaluate if the use of an individualized respiratory management strategy encouraging the use of ENCPAP is associated with an increased risk of NEC, and to determine risk factors for NEC in premature infants supported by CPAP. METHODS: A retrospective analysis was conducted on VLBW infants (birth weight < 1500 g) managed at 2 institutions that use an ENCPAP respiratory management strategy for premature infants. Data on the use of oxygen and mode of ventilatory support were collected during the first 3 days of life. Diagnosis of NEC was used as the dependent variable in a logistic regression model. Birth weight, gender, prenatal steroid use, mode of respiratory support (CPAP versus ventilator) and fraction of inspired oxygen, umbilical artery catheter placement, partial pressure of oxygen, patent ductus arteriosus, early sepsis, hospital, and delivery room management (ENCPAP versus initial intubation) were controlled for in the model. RESULTS: Data on 343 premature infants were collected for this study. Mean birth weight was 999 +/- 289 g and gestational age was 28 +/- 2.6 weeks. The majority of patients were managed with ENCPAP, with only 13% of patients intubated in the delivery room. The overall incidence of NEC was 7% (n = 24). The exposure to ENCPAP did not increase the risk for NEC compared with the use of a ventilator. CONCLUSIONS. The risk of NEC in VLBW premature infants was not increased by the use of ENCPAP. Initial respiratory support with ENCPAP seems to be a safe alternative to routine intubation and mechanical ventilation in premature infants.

Established genetic risk factors do not distinguish early and later onset Crohn's disease.

BACKGROUND: Early-onset disease is frequently examined in genetic studies because it is presumed to contain a more severe subset of patients under a higher influence of genetic effects. In light of the dramatic success of Crohn's disease (CD) gene discovery efforts, we aimed to characterize the contribution of established common risk variants to pediatric CD. METHODS: Using 35 confirmed CD risk alleles, we genotyped 384 parent-child trios (mean age of onset 11.7 years) along with 321 healthy controls. We performed association tests on the independent pediatric cohort and compared results to those previously published.1 We also computed a weighted CD genetic risk score for each affected person. Six variants not previously validated in children (at 5q33, 1q24, 7p12, 12q12, 8q24, and 1q32) were significantly associated with pediatric CD (P < 0.03). RESULTS: We detected no significant association between risk score and age at onset through age 30. This analysis illustrates that the genetic effect of established CD risk variants is similar in early and later onset CD. CONCLUSIONS: These results motivate joint analyses of genome-wide association data in early and late onset cohorts and suggest that, rather than established risk variants, independent variants or environmental exposures should be sought as modulators of age of onset.