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Article
Prospective characterization of intestinal MRI intravoxel incoherent motion in pediatric and young adult patients with newly diagnosed small bowel Crohn’s disease
MRI diffusion-weighted imaging (DWI) is commonly used in MR enterography protocols for assessment of intestinal inflammation in patients with Crohn’s disease. The intravoxel incoherent motion (IVIM) approach t...
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Article
Imaging and clinical predictors of surgery in stricturing ileal Crohn’s disease: a retrospective study from a large pediatric hospital
(1) To determine the frequency of surgical management in children with Crohn's Disease (CD) and a new radiologic ileal stricture, and (2) to identify imaging and clinical features that predict the need for sur...
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Article
Open AccessReduced LHFPL3-AS2 lncRNA expression is linked to altered epithelial polarity and proliferation, and to ileal ulceration in Crohn disease
Disruption of intestinal epithelial functions is linked to Crohn disease (CD) pathogenesis. We identified a widespread reduction in the expression of long non-coding RNAs (lncRNAs) including LHFPL3-AS2 in the tre...
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Article
Open AccessIdentifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews....
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Article
Open AccessLongitudinal DNA methylation profiling of the rectal mucosa identifies cell-specific signatures of disease status, severity and clinical outcomes in ulcerative colitis cell-specific DNA methylation signatures of UC
In peripheral blood, DNA methylation (DNAm) patterns in inflammatory bowel disease patients reflect inflammatory status rather than disease status. Here, we examined DNAm in diseased rectal mucosa from ulcerat...
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Article
Ultrasound shear wave elastography in pediatric stricturing small bowel Crohn disease: correlation with histology and second harmonic imaging microscopy
Preclinical animal as well as small exploratory ex vivo and in vivo human studies have suggested that bowel wall shear wave speed (SWS) measurements may be a noninvasive biomarker of intestinal damage.
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Article
Open AccessNutritional deficiency in an intestine-on-a-chip recapitulates injury hallmarks associated with environmental enteric dysfunction
Environmental enteric dysfunction (EED)—a chronic inflammatory condition of the intestine—is characterized by villus blunting, compromised intestinal barrier function and reduced nutrient absorption. Here we s...
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Article
Bowel wall MRI T1 relaxation estimates for assessment of intestinal inflammation in pediatric Crohn’s disease
To compare bowel wall T1 relaxation estimates in young patients with newly diagnosed ileal CD to healthy control participants, characterize their change over time in response to biologic medical therapy, and e...
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Article
Open AccessProfiling non-coding RNA levels with clinical classifiers in pediatric Crohn’s disease
Crohn’s disease (CD) is a heritable chronic inflammatory disorder. Non-coding RNAs (ncRNAs) play an important role in epigenetic regulation by affecting gene expression, but can also directly affect protein fu...
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Article
Open AccessPredicting disease course in ulcerative colitis using stool proteins identified through an aptamer-based screen
In the search for improved stool biomarkers for inflammatory bowel disease (IBD), an aptamer-based screen of 1129 stool proteins was conducted using stool samples from an IBD cohort. Here we report that of the...
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Article
Microbiota-derived metabolite promotes HDAC3 activity in the gut
The coevolution of mammalian hosts and their beneficial commensal microbes has led to development of symbiotic host–microbiota relationships1. Epigenetic machinery permits mammalian cells to integrate environment...
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Article
Open AccessDefining the Celiac Disease Transcriptome using Clinical Pathology Specimens Reveals Biologic Pathways and Supports Diagnosis
Celiac disease is provoked by gluten exposure, but the complete pathogenic process in the duodenum and the loss of tolerance to gluten is not well understood. We aimed to define the core celiac transcriptomic ...
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Article
Prioritizing Crohn’s disease genes by integrating association signals with gene expression implicates monocyte subsets
Genome-wide association studies have identified ~170 loci associated with Crohn’s disease (CD) and defining which genes drive these association signals is a major challenge. The primary aim of this study was t...
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Article
Open AccessStudy of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Environmental Enteropathy (EE), characterized by alterations in intestinal structure, function, and immune activation, is believed to be an important contributor to childhood undernutrition and its associated ...
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Article
Open AccessNeutrophil GM-CSF signaling in inflammatory bowel disease patients is influenced by non-coding genetic variants
Neutrophil dysfunction and GM-CSF auto-antibodies are observed in pediatric and adult patients with Crohn’s disease (CD). We associated damaging coding variants with low GM-CSF induced STAT5 stimulation index ...
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Article
Open AccessMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneo...
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Article
Open AccessGenetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort
In the United States, approximately 5% of individuals with inflammatory bowel disease (IBD) are younger than 20 years old. Studies of pediatric cohorts can provide unique insights into genetic architecture of ...
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Article
Open AccessUlcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response
Molecular mechanisms driving disease course and response to therapy in ulcerative colitis (UC) are not well understood. Here, we use RNAseq to define pre-treatment rectal gene expression, and fecal microbiota ...
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Article
Penetrating Crohn disease: does it occur in the absence of stricturing disease?
To establish the relationship between penetrating complications and bowel luminal narrowing/stricturing disease in pediatric Crohn disease (CD).
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Article
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset ...
