MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility

Peck, Bailey C. E. BA*,†; Weiser, Matthew BS*,‡; Lee, Saangyoung E. BS§; Gipson, Gregory R. BS§; Iyer, Vishal B.§; Sartor, Ryan B. MD§; Herfarth, Hans H. MD, PhD§; Long, Millie D. MD, MPH§; Hansen, Jonathan J. MD, PhD§; Isaacs, Kim L. MD, PhD§; Trembath, Dimitri G. MD||; Rahbar, Reza MD; Sadiq, Timothy S. MD; Furey, Terrence S. PhD*,‡,**,††; Sethupathy, Praveen PhD*,†,‡,**; Sheikh, Shehzad Z. MD, PhD*,†,§

Inflammatory Bowel Diseases:
doi: 10.1097/MIB.0000000000000478
Future Directions and Methods for IBD Research
Abstract

Background: There is a dire need for reliable prognostic markers that can guide effective therapeutic intervention in Crohn's disease (CD). We examined whether different phenotypes in CD can be classified based on colonic microRNA (miRNA) expression and whether miRNAs have prognostic utility for CD.

Methods: High-throughput sequencing of small and total RNA isolated from colon tissue from patients with CD and controls without Inflammatory Bowel Disease (non-IBD) was performed. To identify miRNAs associated with specific phenotypes of CD, patients were stratified according to disease behavior (nonstricturing, nonpenetrating; stricturing; penetrating), and miRNA profiles in each subset were compared with those of the non-IBD group. Validation assays were performed using quantitative reverse transcription polymerase chain reaction. These miRNAs were further evaluated by quantitative reverse transcriptase polymerase chain reaction on formalin-fixed, paraffin-embedded tissue (index biopsies) of patients with nonpenetrating CD at the time of diagnosis that either retained the nonpenetrating phenotype or progressed to penetrating/fistulizing CD.

Results: We found a suite of miRNAs, including miR-31-5p, miR-215, miR-223-3p, miR-196b-5p, and miR-203 that stratify patients with CD according to disease behavior independent of the effect of inflammation. Furthermore, we also demonstrated that expression levels of miR-215 in index biopsies of patients with CD might predict the likelihood of progression to penetrating/fistulizing CD. Finally, using a novel statistical simulation approach applied to colonic RNA-sequencing data for patients with CD and non-IBD controls, we identified miR-31-5p and miR-203 as candidate master regulators of gene expression profiles associated with CD.

Conclusions: miRNAs may serve as clinically useful prognostic markers guiding initial therapy and identifying patients who would benefit most from effective intervention.

In Brief

Article first published online 6 July 2015.

Author Information

*Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;

Department of Medicine, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;

Department of Medicine, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;

§Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;

Departments of ||Pathology and

Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina;

**Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and

††Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

Reprints: Shehzad Z. Sheikh, MD, PhD, Department of Medicine and Genetics, University of North Carolina at Chapel Hill, 7340B Medical Biomolecular Research Building, 101 Mason Farm Road, Chapel Hill, NC 27517 (e-mail: sheisx@med.unc.edu); Terrence S. Furey, PhD, Departments of Genetics and Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 (e-mail: tsfurey@email.unc.edu); and Praveen Sethupathy PhD, Department of Genetics, University of North Carolina at Chapel Hill, 5091 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 (e-mail: praveen_sethupathy@med.unc.edu).

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The authors have no conflicts of interest to disclose.

Supported by American Gastroenterological Association (AGA) Research Scholar Award (SZS), Broad Medical Research Program (SZS), Crohn's and Colitis Foundation of America's Career Development Award (SZS) and Microbiome Consortium (RBS), R01-ES024983 from NIEHS (MW, SZS, and TSF), P01-DK094779-01A1 from NIDDK (RBS and SZS), P30-DK034987 from NIDDK (RBS and SZS), R00-DK09131802 from NIDDK (PS), UNC Nutrition Obesity Research Center Pilot & Feasibility Grant P30DK056350 (PS), UNC Genetics and Molecular Biology T32 Training Grant GM00709239 (BCEP), SHARE from the Helmsley Trust and UNC Institute for Maximizing Student Diversity Excellence Fellowship R25-GM05533613 (BCEP). The UNC Translational Pathology Laboratory is supported in part by grants from the National Cancer Institute (3P30CA016086) and the UNC University Cancer Research Fund (UCRF).

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Received March 17, 2015

Accepted April 14, 2015

© Crohn's & Colitis Foundation of America, Inc.