Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder that affects up to 15% of adults, predominantly women, in the United States. Symptoms include chronic or recurrent abdominal pain associated with diarrhea, constipation or both. It is considered a stress-sensitive disorder that is associated with altered brain-gut interactions. Biomarkers that can reliably diagnose IBS or monitor treatment response are currently lacking. The current proposal is based on our preliminary data that epigenetic markers, namely DNA methylation, can distinguish IBS patients from healthy individuals. DNA methylation is a key epigenetic mechanism that governs vertebrate gene function. It has emerged as a leading mechanism linking gene- environment interactions to long-term behavioral development, particularly in complex disorders such as IBS. Our preliminary data on genome-wide DNA methylation for peripheral blood mononuclear cells (PBMCs) in a limited number of subjects (IBS: N=12, healthy controls: N=12) identified a set of epigenetic markers located on genes including SSPO, RNF39, GSTM1, GSTM5, TPPP and SNCAIP that can potentially distinguish IBS patients from healthy controls. Gene ontology analysis showed an enrichment of genes involved in neuropeptide pathways. We validated the differential methylation of CpG sites in these genes using bisulphite sequencing. However, these findings need to be replicated and validated in a larger cohort. Therefore, the studies proposed here are intended to identify robust epigenetic biomarkers for an accurate diagnosis of IBS and to gain critical insights into the pathogenesis of this disorder.
Our aims are to: 1) Identify DNA methylation based biomarkers using genome-wide DNA methylation profiling in peripheral blood mononuclear cells (PBMCs) in IBS. 2) Study genome-wide methylation and expression differences in colon tissue of IBS patients and HCs.
In Aim 1, we will conduct a genome-wide DNA methylation profiling in a larger, independent cohort of IBS patients (N=108) and controls (N=36) replicate the differential methylation of selected markers in a subset of samples using an affordable technique (MethyLight PCR) that can be employed for the routine diagnosis of IBS.
In Aim 2, we propose genome-wide DNA methylation and gene expression profiling of banked colonic mucosal biopsies collected from IBS patients (N=108) and controls (N=36) to investigate epigenetically deregulated genes and associated pathways, which can give important insights on pathophysiology of IBS.

Public Health Relevance

This project will provide new insights into the pathogenesis and diagnosis of irritable bowel syndrome (IBS), which is one of the most common gastrointestinal conditions seen in primary care and gastroenterology practices. The proposed studies expand on the insights gained from our preliminary data that identified a set of epigenetic markers that can potentially distinguish IBS patients from healthy controls and aim at identifying potential biomarkers in the different IBS bowel habit subtypes and their association with IBS symptoms. The studies will provide an unprecedented wealth of data, which will allow for a breakthrough in our understanding of IBS pathophysiology and may lead to the identification of novel diagnostic biomarkers and potential targets for drug discovery.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Exploratory/Developmental Grants (R21)
Project #
1R21DK104078-01A1
Application #
8968752
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Hamilton, Frank A
Project Start
2015-08-01
Project End
2017-07-31
Budget Start
2015-08-01
Budget End
2016-07-31
Support Year
1
Fiscal Year
2015
Total Cost
Indirect Cost
Name
University of California Los Angeles
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Mahurkar, S; Polytarchou, C; Iliopoulos, D et al. (2016) Genome-wide DNA methylation profiling of peripheral blood mononuclear cells in irritable bowel syndrome. Neurogastroenterol Motil 28:410-22