Research Projects

Pediatric onset CD is the fastest growing incident age group as is considered to be a more aggressive phenotype than adult onset disease. At presentation, the most of the children present with an inflammatory or so called non-complicated disease behavior. Over time a sub-group of CD patients progress to more a complicated disease behavior, which involve hospitalization and sometimes surgery. The factors or pathogenic mechanisms underlying the development of complications are poorly understood. Therefore, discovery of predictive factors contributing to the progression of a CD patient from an uncomplicated to complicated phenotype necessitates engaging a patient population naïve to all therapies and devoid of any confounding factors. In 2008 the RISK (Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn’s Disease) study was commenced at 28 investigative centers in North America with the goal of prospectively characterizing and predicting the natural history of newly diagnosed CD in children presenting with uncomplicated disease.

To this end, over 1000 CD patients have been prospectively enrolled at this study. Each patient was followed for over 5 years. All patients were required to undergo a baseline colonoscopy before treatment with findings recorded in a standardized fashion. At enrollment and during ongoing prospective follow-up evaluation, medication exposure, clinical, radiological, endoscopic and laboratory data were obtained for each enrolled patient and submitted to a centralized data management center. All patients were managed according to the dictates of their physicians, not by standardized protocols. The institutional review board of each site reviewed and approved the protocol and each participant provided written informed consent. Blood for genomic DNA, serology, stool and biopsy samples were collected at the time of diagnosis in all subjects. Patients were followed up at minimum of every 6 months. During the follow up visits for up to 3 years, blood samples and (on occasion) ileal biopsy were collected. Currently our team is working towards the primary aim of the project, which is to develop a composite risk score using phenotypes, genetics, serology, microbiome and gene expression markers.

Funding provided by Crohn’s and Colitis Foundation of America (CCFA)

Nearly all genetic studies of IBD are focused on Caucasians; however, there is emerging data suggesting that the disease burden is similar in African Americans (AA). Variation data from HapMap, 1000 Genomics, and other disease studies suggests that the allelic architecture of AA populations could be significantly different from Caucasians.  A large sample size is needed for an adequately powered genetic study.  Additionally, the AA population has much more genetic variation.  We are currently in alliance with the NIDDK IBD Genetics Consortium’s (IBDGC) mission to dramatically increase the recruitment of AA patients (pediatric and adult) IBD subjects for gene discovery purposes.

_{Funding provided by National Institutes of Health (NIH/NIDDK) R01DK087694}

Epigenetic modifications induce changes in gene expression through structural alterations of DNA that are maintained through each round of cell division; they respond to changes in the environment, are potentially reversible and can be targeted for disease therapies. DNA methylation at cytosine-guanine dinucleotides (CpG sites) is the epigenetic modification that is most commonly studied in humans. It regulates gene expression by influencing the recruitment and binding of regulatory proteins to DNA. Typically, an increase in methylation at gene promoter regions correlates with a decrease in expression of that gene Intragenic DNA methylation is also important to regulate alternative promoters and enhancers that define a variety of alternative transcripts.

•  Aim 1: Characterize DNA methylation differences over the course of treatment in pediatric Crohn’s cases over 3 years of treatment.
•  Aim 2: Characterize epigenetic markers in intestinal tissue to assess the utility of both whole blood and intestinal methylation patterns as biomarkers to predict side effects following treatment.

_{Funding provided by National Institutes of Health (NIH/NIDDK) R21DK119997}

We will use this cohort to evaluate and validate the utility of dropout-based computational methods for single-cell RNA-seq analysis in the context of Crohn’s disease (CD). Crohn’s disease is a chronic inflammatory disease, characterized by remitting relapsing inflammation affecting transmurally – that is, the inflammation goes beyond the mucosa, necessitating mapping of epithelial cells along with the immune and non-immune cells of the lamina propria to observe the complete picture. We will obtain colonoscopically pinch mucosal biopsies from CD and controls, as this provides the needed cells from mucosa and sub-mucosa. Although CD can affect any part of the gut, terminal ileum biopsies are proposed here, because the ileum is involved in 70% or more of subjects with CD. Since the status of active inflammation can greatly influence the transcriptomic profiles of each cell type in the gut, an ideal experiment should include samples representing the active stage (inflamed), inactive stage (non-inflamed), and compared with non-disease normal control. We also aim to explore racial and ethnic contributions to variability in scRNA-seq in the gut pertaining to CD pathology.

• Aim 1: Generate scRNA-seq data from Crohn’s patients using gut tissue.

• Aim 2: Apply and compare co-occurrence clustering and Seurat to the scRNA-seq data.

• Aim 3: Compare the heterogeneity across the three proposed sample groups.

_{Funding provided by The Leona M. and Harry B. Helmsley Charitable Trust}