Emory University School of Medicine

Aim 1: Define the genetic architecture of IBD in AA by greatly expanding the IBD-GC AA sampling, developing an inception AA cohort, and evaluating PRS×Environment interactions.

1a. Building on our established program for recruitment and retention of AA with IBD into genetic research studies, we will exponentially increase the AA sample size by direct-to-patient recruitments, web-based consenting, and salivary DNA- an innovative approach that will recruit large numbers of AA.

1b. An inception cohort of treatment naïve AA with multiple time point biospecimen collections.

1c. We will generate African-specific PRS using recently published prediction methods for weighting effect sizes and evaluate the interactions of anthropometric (BMI as an example) and other environmental factors such as smoking in determining whether disease severity at diagnosis and during the follow-up varies as a function of polygenic risk in AA.

Aim 2: To test the hypothesis that a subset of ileo-colonic methylation signatures is consistent with a role in IBD onset and/or severity, rather than an outcome of IBD, and determine whether these signatures are independent of, or interacting with, the environmental factors of the cohort outlined in Aim 1B.

2a. Whole epigenome methylation profiles will be generated by MethylationEPIC BeadChip arrays at diagnosis and 12-month follow-up from rectal and ileal biopsies and compare with European-ancestry IBD patients.

2b. Hypothesis testing will evaluate whether (i) our signature of IBD-associated methylation is ancestry-biased, (ii) behaves to a similar degree across ancestries, (iii) is predictive of adverse outcomes, and (iv) interacts with or is independent of environmental contributors.

Aim 3: To define gut microbiome-metabolome interactions that promote disease in AA.

3a. Discover and validate ileo-colonic metabolomic signatures of IBD progression in AA, using Mendelian randomization to establish likely causal mechanisms, and identify microbiome mediators of metabolic diversity in matched fecal samples.

3b. Pilot investigation of the impact of disease-associated metabolites on epithelial cell function contrasting AA and EA patient-derived organoids by histological and single cell RNAseq criteria.

• Biorepository Center: We have an extensive collection of approximately 3200 biopsies including ileal and rectal sites, 100 organoids, and 50 MSC cultures from biopsies of various disease states are available for experimentation. We also have DNA and RNA from whole blood and serum/plasma for all the described samples. Existing and newly obtained samples from the blood and tissue will be processed for multi-omic analysis as well as extensive repeated phenotyping and polygenetic/multi-omic risk prediction and validation. All samples that are received in the lab are de-identified, stored and tracked across the life of each project using a Nautilus Laboratory Information Management System (LIMS) designed by ThermoLab Systems.

• Patient recruitment: Children’s Healthcare of Atlanta (CHOA) is a 530-bed tertiary care, highly specialized children’s hospital (both Egleston and Scottish Rite campuses). Specifically, the Pediatric Gastroenterology Division encompasses 19 attending physicians, and 13 clinical nurses for outpatient and inpatient clinical and endoscopic services. The pediatric hospitals & clinics currently follows about 1800 children with IBD and is expected to continue at a rate of about 150-200 new diagnosis of IBD per year. As 60% of the population within Atlanta are of AA ancestry, we have the advantage of recruiting more AA patients to address the unmet need of studying disease manifestations in this population. In terms of clinical volume, about 15,000 out-patient visits will occur by GI practices, suppling a rich source of clinical material for Dr. Kugathasan’s research efforts. The adult gastroenterology service at Emory University covers Emory University Hospital/clinics, Saint Joseph’s Hospital/Clinics and Grady Hospital/ clinics and VA hospitals. It encompasses 10 attending physicians and follows about 3350 patients with IBD of which 1675 patients carry an IBD diagnosis. Approximately 60% of the 1675 patients are self-identified as AA, making a little over 1000 AA subjects being followed with the diagnosis of IBD.

• Data management: All study data is collected via REDCap and complies with applicable guidelines regarding patient confidentiality and data integrity.

Our overall research goals are to further extend novel genetic discoveries in inflammatory bowel disease (IBD). We are particularly eager to explore these aspects specific to African Americans (AAs) with IBD, who have been noticeably understudied across any genomic research although they currently make up nearly 15% of the US population, 28 % of Georgia population and 60% of city of Atlanta. Though underrepresented minorities – including African Americans – continue to grow throughout the United States, less than 2% of any genetic/genomic research studies have focused on subjects with African American ancestry. African Americans with IBD are known to exhibit severe phenotypes and worst outcomes. Our recent studies have also demonstrated that European American (EA) polygenic risk scores (PRS) cannot be extended to patients of AA ancestry, and more specific AA ancestry-based scoring is required. In the past 10 years, our center alone has been able to enroll a little over 1500 cases of AAs with IBD, which comprises ~50% of all AAs studied in the NIDDK IBDGC. In this present study, we aim to expand the IBDGC sampling of AAs by recruitment through our site and through numerous participating satellite sites. The following are areas of research we wish to address in order to obtain a deeper understanding of the presentation of AAs with IBD and to eventually develop AA-specific diagnostic biomarkers for personalized therapies.

•     Genomics: GWAS studies have identified about 250 IBD loci that have contributed to significant risk for IBD disease susceptibility. Our studies have determined that while many of these loci are shared between IBD patients of AA and EA ancestry, there are also significant differences in polygenic risk scores (PRS). These race-specific variations impacting allele frequencies and effect sizes call for a need to develop African-ancestry specific risk assessments. We will obtain blood and/or salivary DNA samples from expanding the recruitment of AA patients with IBD in our inception cohort, with the aim of better comprehending AA-specific genetic architecture in IBD.

•     DNA methylation: To further explore the influence of epigenetic alterations in IBD, we have assessed DNA methylation in blood and intestine that lead to IBD. Our previous studies have indicated that for Crohn’s disease, DNA methylation-associated patterns correspond to inflammatory features rather than disease development and progression. Current treatments for IBD have primarily targeted the immune system, and nearly half of all IBD patients lack effective response to these treatments. We will use methylation pattern analyses from mucosa and blood as stated in Aim 2 to potentially identify new targets beyond the immune system.

•     Enteroid models: In order to understand changes in the function of the intestinal epithelium and its role in IBD, we have utilized patient-derived organoids grown from mucosal biopsies. These cultured organoids have demonstrated disease-specific signatures at the transcript and secretome level, and we have found pharmaceutical targets that could potentially reverse these signatures. Our studies have recognized that targeting the epithelium may reverse a stricturing phenotype of this disease. The role of the epithelium has also been highlighted in studies of genomic DNA methylation patterns within the rectum of IBD patients, supporting the use of patient-derived organoids for target discovery within IBD. In this current study, we aim to use these organoid models to additionally compare microbiome-metabolome interactions between AA and EA samples.

•     Transcriptomics: Although several bulk biopsy transcriptomic studies have been conducted for IBD, those studies evaluated the whole tissue for analysis of specific phenotypes and relevant pathways. To enable precision medicine advances in IBD, single-cell technologies have been leveraged. Our recent analysis highlights the heterogeneity amongst subjects within the same disease phenotype (treatment-naive and established Crohn’s Disease patients), shining new light on personalized treatment responses and strategies.

•     Other ongoing major studies in the lab include combining cutting-edge technologies such as spatial transcriptomics and ATAC- seq to further comprehend patient-specific signatures.

•     Intestine derived mesenchymal stromal cells (MSCs) have also been characterized and banked within our biorepository. These MSCs from over 50 patients have been evaluated for their therapeutic potential. To understand immunological aspects of IBD, immune cells have been isolated from the intestine of remission and refractory patients with Crohn’s disease. These cells have been characterized to understand immune mediators involved in resistance to anti-TNF therapy.

The insights from these studies will offer the opportunity to serve the unmet need of more personalized therapeutics for patients with IBD. A multi-omics approach in experimentation and analysis will be conducted by experienced personnel. Combining this expertise with the availability of rich resources at Emory will culminate in discovering new avenues for understanding IBD disease course— from disease onset throughout its progression.