Joshua D. Noe

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. We identified core gene expression profiles and microbial communities in the affected CD ilea that are preserved in the unaffected ilea of patients with colon-only CD but not present in those with UC or control individuals; therefore, this signature is specific to CD and independent of clinical inflammation. An abnormal increase of antimicrobial dual oxidase (DUOX2) expression was detected in association with an expansion of Proteobacteria in both UC and CD, while expression of lipoprotein APOA1 gene was downregulated and associated with CD-specific alterations in Firmicutes. The increased DUOX2 and decreased APOA1 gene expression signature favored oxidative stress and Th1 polarization and was maximally altered in patients with more severe mucosal injury. A regression model that included APOA1 gene expression and microbial abundance more accurately predicted month 6 steroid-free remission than a model using clinical factors alone. These CD-specific host and microbe profiles identify the ileum as the primary inductive site for all forms of CD and may direct prognostic and therapeutic approaches.

Retrospective Evaluation of the Safety and Effect of Adalimumab Therapy (RESEAT) in Pediatric Crohn’s Disease

OBJECTIVES:Adalimumab, an anti-tumor necrosis factor immunoglobulin-1 antibody, is increasingly being reported as a potential treatment option for children with moderate-to-severe Crohn’s disease (CD). The aim of this study was to characterize common indications, safety, tolerability, and clinical response to adalimumab in pediatric CD in a large, multicenter, patient cohort.METHODS:Data were obtained using a retrospective, uncontrolled chart review at 12 sites of the Pediatric Inflammatory Bowel Disease Collaborative Research Group. Clinical, laboratory, and demographic data were obtained for CD patients who received at least one dose of adalimumab. Indication for adalimumab, concomitant medications, and clinical outcome at 3, 6, and 12 months for each patient were recorded using physician global assessment (PGA) and Pediatric CD Activity Index scores. Serious adverse events were identified.RESULTS:A total of 115 patients (54% female) received at least one dose of adalimumab. The mean age at the diagnosis of CD was 11.1±3.1 years, with the first adalimumab dose administered at 4.7±2.8 years after diagnosis. The most common dosing frequency was every other week with induction doses of 160/80 mg in 19%, 80/40 mg in 44%, and 40/40 mg in 15% of patients. Maintenance dosing was 40 mg every other week in 88% of patients. Mean follow-up after initial adalimumab dose was 10±8.6 months. Infliximab treatment preceded adalimumab in 95% of patients, with a mean of 12 infliximab infusions (range: 1–44). Infliximab discontinuation was due to loss of response (47%), infusion reaction or infliximab intolerance (45%), or preference for a subcutaneous medication (9%). Concomitant medications at the commencement of adalimumab were corticosteroids (38%), azathioprine/6-mercaptopurine (41%), and methotrexate (23%). Clinical response measured by PGA at 3, 6, and 12 months was 65, 71, and 70%, respectively, with steroid-free remission at 3, 6, and 12 months of 22, 33, and 42%, respectively. There were no malignancies, serious infections, or deaths in the study subjects.CONCLUSIONS:Adalimumab was a well-tolerated and effective rescue therapy for moderate-to-severe pediatric CD patients previously treated with infliximab. Adalimumab demonstrated a steroid-sparing effect, and >70% of patients achieved rapid response that was sustained through 12 months.

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study

BACKGROUND Stricturing and penetrating complications account for substantial morbidity and health-care costs in paediatric and adult onset Crohns disease. Validated models to predict risk for complications are not available, and the effect of treatment on risk is unknown. METHODS We did a prospective inception cohort study of paediatric patients with newly diagnosed Crohns disease at 28 sites in the USA and Canada. Genotypes, antimicrobial serologies, ileal gene expression, and ileal, rectal, and faecal microbiota were assessed. A competing-risk model for disease complications was derived and validated in independent groups. Propensity-score matching tested the effect of anti-tumour necrosis factor α (TNFα) therapy exposure within 90 days of diagnosis on complication risk. FINDINGS Between Nov 1, 2008, and June 30, 2012, we enrolled 913 patients, 78 (9%) of whom experienced Crohns disease complications. The validated competing-risk model included age, race, disease location, and antimicrobial serologies and provided a sensitivity of 66% (95% CI 51-82) and specificity of 63% (55-71), with a negative predictive value of 95% (94-97). Patients who received early anti-TNFα therapy were less likely to have penetrating complications (hazard ratio [HR] 0·30, 95% CI 0·10-0·89; p=0·0296) but not stricturing complication (1·13, 0·51-2·51; 0·76) than were those who did not receive early anti-TNFα therapy. Ruminococcus was implicated in stricturing complications and Veillonella in penetrating complications. Ileal genes controlling extracellular matrix production were upregulated at diagnosis, and this gene signature was associated with stricturing in the risk model (HR 1·70, 95% CI 1·12-2·57; p=0·0120). When this gene signature was included, the models specificity improved to 71%. INTERPRETATION Our findings support the usefulness of risk stratification of paediatric patients with Crohns disease at diagnosis, and selection of anti-TNFα therapy. FUNDING Crohns and Colitis Foundation of America, Cincinnati Childrens Hospital Research Foundation Digestive Health Center.

Short‐term response to adalimumab in childhood inflammatory bowel disease

Background: Adalimumab is effective for adults with moderate to severe Crohns disease (CD). Data in children with inflammatory bowel disease (IBD) is sparse. We aim to evaluate pediatric IBD response to adalimumab. Methods: We conducted a retrospective chart review of pediatric IBD patients treated with adalimumab. We defined response as either a decrease in the disease activity index severity or remission after 3–6 months of treatment. Results: Ten patients were identified. Seven had CD, three had ulcerative colitis (UC). All had colonic disease and disease in either the esophagus, stomach, or duodenum. Eight patients initially responded to infliximab, 5 with CD and 3 with UC; 2 CD patients had incomplete data for evaluation. The mean and median times between initial infliximab and initial adalimumab were 29.5 and 24 months, respectively. Eight patients responded to adalimumab 40 mg or 80 mg biweekly, or 80 mg initial dose followed by 40 mg biweekly. The mean Pediatric Crohns Disease Activity Index (PCDAI) in CD patients before and after adalimumab were 12 and 4.2, respectively (normal ≤10). The mean Lichtiger Colitis Activity Index (LCAI) in UC patients before and after adalimumab were 9 and 5.1, respectively (normal <10). Corticosteroids were weaned off in 4/7 patients at 1 to 10 months after initiation of adalimumab. One patient with CD and 1 patient with UC failed adalimumab, required surgery, and remained on corticosteroids. Conclusions: Adalimumab is useful in pediatric IBD patients who become intolerant of infliximab.

Identifying youth nonadherence in clinical settings: Data-based recommendations for children and adolescents with inflammatory bowel disease†

Background: To examine the validity of patient self‐report of thiopurine adherence in pediatric inflammatory bowel disease (IBD) against an objective electronic monitoring adherence measure, and to investigate the role of youth and maternal involvement in remembering to take daily medications as predictors of medication adherence. Methods: Fifty‐one youths with IBD, ages 11–18 years, participated. Youths completed questionnaire assessments of their own and their maternal caregivers involvement in remembering to take daily medications at baseline, completed monthly interviews assessing thiopurine adherence over the past week for a period of 6 months, and utilized a Medication Events Monitoring System (MEMS) electronic monitor for their thiopurine medication for 6 months. Participants were grouped into adherent (at least 80% of doses taken based on objective MEMS caps) or nonadherent for analyses. Results: Youths who were nonadherent based on electronic monitoring overestimated their adherence by 23%, whereas adherent youths overestimated their adherence by only 2%, and as such patient self‐report offered little utility in identifying youths who were nonadherent. Youths who reported high levels of involvement in remembering to take their medications were nearly eight times less likely to be nonadherent. Conclusions: The current findings provide evidence that clinicians who work with children and adolescents with IBD may benefit from modifying their approach to nonadherence screening. Asking about youth involvement in remembering daily medications may be more informative than asking them to recall their medication‐taking behavior over the last week in identifying those at highest risk for nonadherence. (Inflamm Bowel Dis 2011;)

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.

Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease

Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohns disease. We show that TRSs based on genes regulated by variants linked to inflammatory bowel disease (IBD) not only outperform genetic risk scores (GRSs) in distinguishing Crohns disease from healthy samples, but also serve to identify patients who in time will progress to complicated disease. Our dissection of eQTL effects may be used to distinguish genes whose association with disease is through promotion versus protection, thereby linking statistical association to biological mechanism. The TRS approach constitutes a potential strategy for personalized medicine that enhances inference from static genotypic risk assessment.

Navigating recurrent abdominal pain through clinical clues, red flags, and initial testing.

Recurrent abdominal pain is a common chronic complaint that presents to your office. The constant challenge is one of detecting those with organic disease from the majority who have a functional pain disorder including functional dyspepsia, irritable bowel syndrome, functional abdominal pain, and abdominal migraine. Beginning with a detailed history and physical exam, you can: 1) apply the symptom-based Rome III criteria to positively identify a functional disorder, and 2) filter these findings through the diagnostic clues and red flags that point toward specific organic disease and/or further testing. Once a functional diagnosis has been made or an organic disease is suspected, you can initiate a self-limited empiric therapeutic trial. With this diagnostic approach, you should feel confident navigating through the initial evaluation, management, and consultation referral for a child or adolescent with recurrent abdominal pain.

Paneth cell defects in Crohn’s disease patients promote dysbiosis

BACKGROUND Paneth cell dysfunction has been implicated in a subset of Crohns disease (CD) patients. We previously stratified clinical outcomes of CD patients by using Paneth cell phenotypes, which we defined by the intracellular distribution of antimicrobial proteins. Animal studies suggest that Paneth cells shape the intestinal microbiome. However, it is unclear whether Paneth cell phenotypes alter the microbiome complexity in CD subjects. Therefore, we analyzed the correlation of Paneth cell phenotypes with mucosal microbiome composition and ileal RNA expression in pediatric CD and noninflammatory bowel disease (non-IBD) patients. METHODS Pediatric CD (n = 44) and non-IBD (n = 62) patients aged 4 to 18 were recruited prior to routine endoscopic biopsy. Ileal mucosal samples were analyzed for Paneth cell phenotypes, mucosal microbiome composition, and RNA transcriptome. RESULTS The prevalence of abnormal Paneth cells was higher in pediatric versus adult CD cohorts. For pediatric CD patients, those with abnormal Paneth cells showed significant changes in their ileal mucosal microbiome, highlighted by reduced protective microbes and enriched proinflammatory microbes. Ileal transcriptome profiles showed reduced transcripts for genes that control oxidative phosphorylation in CD patients with abnormal Paneth cells. These transcriptional changes in turn were correlated with specific microbiome alterations. In non-IBD patients, a subset contained abnormal Paneth cells. However, this subset was not associated with alterations in the microbiome or host transcriptome. CONCLUSION Paneth cell abnormalities in human subjects are associated with mucosal dysbiosis in the context of CD, and these changes are associated with alterations in oxidative phosphorylation, potentially in a feedback loop. FUNDING The research was funded by Helmsley Charitable Trust (to T.S. Stappenbeck, R.J. Xavier, and D.P.B. McGovern), Crohns and Colitis Foundation of America (to N.H. Salzman, T.S. Stappenbeck, R.J. Xavier, and C. Huttenhower), and Doris Duke Charitable Foundation grant 2014103 (to T.C. Liu).

Can You Teach a Teen New Tricks? Problem Solving Skills Training Improves Oral Medication Adherence in Pediatric Patients with Inflammatory Bowel Disease Participating in a Randomized Trial.

Background:Medication nonadherence is associated with higher disease activity, greater health care utilization, and lower health-related quality of life in pediatric inflammatory bowel diseases (IBD). Problem solving skills training (PSST) is a useful tool to improve adherence in patients with chronic diseases but has not been fully investigated in IBD. This study assessed feasibility, acceptability, and preliminary efficacy of PSST in pediatric IBD. Methods:Recruitment occurred during outpatient clinic appointments. After completion of baseline questionnaires, families were randomized to a treatment group or wait-list comparison group. The treatment group received either 2 or 4 PSST sessions. Youth health-related quality of life was assessed at 3 time points, and electronic monitoring of oral medication adherence occurred for the study duration. Results:Seventy-six youth (ages 11–18 years) on an oral IBD maintenance medication participated. High retention (86%) and treatment fidelity rates (95%) supported feasibility. High satisfaction ratings (mean values ≥4.2 on 1–5 scale) supported intervention acceptability. Modest increases in adherence occurred after 2 PSST sessions among those with imperfect baseline adherence (d = 0.41, P < 0.10). Significant increases in adherence after 2 PSST sessions were documented for participants aged 16 to 18 years (d = 0.95, P < 0.05). Improvements in health-related quality of life occurred after 2 PSST sessions. No added benefit of 4 sessions on adherence was documented (d = 0.05, P > 0.05). Conclusions:Phone-delivered PSST was feasible and acceptable. Efficacy estimates were similar to those of lengthier interventions conducted in other chronic illness populations. Older adolescents benefited more from the intervention than their younger counterparts.