PT - JOURNAL ARTICLE AU - Benjamin P. Keith AU - Jasmine B. Barrow AU - Nevzat Kazgan AU - Neil D. Shah AU - Greg R. Gipson AU - Wendy A. Pitman AU - Shruti J. Saxena AU - Elisabeth A. Wolber AU - Matthew S. Schaner AU - Michelle Hoffner O’Connor AU - Omar K. Trad AU - Matthew Kanke AU - Takahiko Toyonaga AU - Nicole Chaumont AU - Timothy S. Sadiq AU - Mark J. Koruda AU - Paul A. Cotney AU - Nancy Allbritton AU - Dimitri G. Trembath AU - Francisco Sylvester AU - Terrence S. Furey AU - Praveen Sethupathy AU - Shehzad Z. Sheikh TI - Association Between Colonic Level of microRNA 31 and Subtypes of Adult and Pediatric Crohn’s Disease AID - 10.1101/307561 DP - 2018 Jan 01 TA - bioRxiv PG - 307561 4099 - http://biorxiv.org/content/early/2018/04/25/307561.short 4100 - http://biorxiv.org/content/early/2018/04/25/307561.full AB - Background & Aims The course of Crohn's disease (CD) is heterogeneous, confounding effective therapy. An analysis of differences in colonic gene expression between patients with vs without CD revealed 2 subsets of patients—a group characterized by genes more highly expressed in the colon (colonlike CD) and a group with increased expression of ileum marker genes (ileum-like CD). We compared differences in microRNAs between these groups.Methods We performed genome-wide microRNA profile analyses of colon tissues from 18 adults with CD and 12 adults without CD (controls). We performed principal component analyses to associate levels of microRNAs with CD subtypes. Colonic epithelial cells and lamina propria immune cells were isolated from intestinal tissues and levels of microRNA 31 (MIR31 or miR-31) were measured by real-time quantitative PCR. We validated the differential expression of miR-31 between the subtypes by measuring miR-31 levels in an independent cohort of 32 adult patients with CD and 23 controls. We generated epithelial colonoid cultures from controls and patients with CD, and measured levels of miR-31 in crypts. We performed genome-wide microRNA profile analyses of formalin-fixed paraffin-embedded colon and ileum biopsies from 76 treatment-naïve pediatric patients with CD and 51 controls and collected data on disease features and outcomes.Results In comparing miRNA expression profiles between 9 patients with colon-like CD and 9 patients with ileum-like CD, we identified 19 miRNAs with significant differences in levels. We observed a 13.5-fold difference in level of miR-31-5p between tissues from patients with colon-like vs ileum-like CD (Padj = 1.43 x 10-18). Principal component analysis found miR-31 to be the top contributor to the variance observed. Levels of miR-31 were increased 60-fold in tissues from patients with ileum-like CD compared with controls (Padj = 2.59 × 10-51). We validated the differential expression of miR-31 between the subtypes in the independent set of tissues. Colonoids derived from patients with CD had significantly higher levels of miR-31 than colonoids derived from control tissues (day 2 P=.041 and day 6 P=.0095). Levels of miR-31 were significantly increased in colon tissues from pediatric patients with CD compared with controls (~7.8-fold, P=4.64 ×10-7) and in ileum tissues from patients with CD vs controls (~1.5-fold, P=9.97 × 10-7). A low level of miR-31 in index biopsies from pediatric patients with only inflammation and no other complications at time of diagnosis associated with development of fibrostenotic ileal CD.Conclusions We identified differences in miR-31 levels in colon tissues from adult and pediatric patients with CD compared with controls, and in patients with ileum-like CD compared with colon-like CD. Further studies are needed to determine the mechanisms by which miR-31 might contribute to pathogenesis of this subtype of CD, or affect response to therapy.Abbreviations used in this papermiRNAmicroRNAqRT-PCRquantitative reverse transcriptase PCRIECIntestinal Epithelial CellRPMMMreads per million mapped to microRNAsFFPEformalin-fixed paraffin embeddedAuthor Contributions: BPK acquired, analyzed and interpreted data, prepared figures, drafted and revised the manuscript. JBB acquired, analyzed and interpreted data and revised the manuscript. NK acquired, analyzed and interpreted data; GRG, MSS, MH, SSS, OKT, PAC, TT, and NA acquired data; and WAP and MK analyzed data. NDS, EAB, NS, TSS, MJK, DGT and FS provided help with tissue acquisition and patient phenotyping. TSF & PS designed the study, analyzed and interpreted the data, drafted and revised the manuscript, and obtained funding. SZS conceptualized and designed the study, acquired the data, interpreted data, drafted and revised the manuscript, obtained funding, acted as study sponsor, and supervised the study. All authors uphold the integrity of the work, have had final approval of the manuscript in its entirety, and are accountable for all aspects of the work.