Background & AimsManagement of Crohn’s disease (CD) requires frequent monitoring for disease activity and response to therapy. In this study, we examined the clinical utility of a novel stool eukaryotic RNA-based (seRNA) diagnostic in patients with CD. MethodsStool samples were collected from 68 individuals for up to three (3) time points prior to and after initiation of an advanced therapy. Stool samples underwent RNA extraction and sequencing using a custom capture panel (n = 1,507 transcripts). Stool-derived eukaryotic RNA (seRNA) signatures were compared to CD activity index (CDAI) scores and endoscopies, when available. Random forest models classified disease severity when compared to CDAI scores. seRNA signatures were also used to assess expression of the therapy target and cell type abundance at various time points. ResultsAcross all 102 samples collected from 68 individuals, the classifier successfully parsed individuals with active disease (n = 37) relative to those in remission (n = 65) with 83% sensitivity and 80% specificity, respectively. A second classifier, which was employed on subjects with active disease (n = 37), successfully parsed individuals with mild disease (n = 15) from those with moderate disease (n = 22) with 89% and 95% sensitivity, respectively. For the 16 subjects with longitudinal data, seRNA expression of the therapeutic target (e.g., ITGA4/ITGB7 for vedolizumab or IL12/IL23 for ustekinumab) as well as lymphocyte burden was correlated with response. ConclusionsA novel seRNA and informatic-based method reliably discriminates active disease from remission and stratifies mild from moderate CD activity. This demonstrates preliminary feasibility to predict therapeutic response and assess disease activity for patients with CD.