DOP89 Pre-treatment mucosal inflammatory and wound healing gene programmes reveal mechanisms associated with future stricturing behaviour during 5-year follow-up in paediatric Crohn’s disease
Authors: Haberman Ziv Y , Minar P , Karns R , Dexheimer P , Ghandikota S , Tegge S , Shapiro D , Shuler B , Venkateswaran S , Braun T , Aronow B , Gibson G , Hyams J , Kugathasan S , Jegga A , Denson L 
Published: January 2020

Abstract

Background
Stricturing complications account for substantial morbidity in Crohn’s disease (CD). We aimed to define ileal gene programmes present at diagnosis in paediatric CD associated with future stricturing behaviour (B2), and to identify potential small molecules to reverse these gene signatures.

Methods
Antimicrobial serologies and ileal gene expression (RNASeq) were assessed at diagnosis in 249 CD patients enrolled in a 5-year inception cohort study. These data were used to define genes associated with stricturing behaviour and for model testing to predict stricturing. Sirius Red immuno-histochemistry was utilised to determine the extent of collagen infiltration into the sub-cryptal space. A bioinformatics approach defined small molecules which may reverse the stricturing gene signature.

Results
Of 249 (8%) patients, 19 developed B2 behaviour during the 5-year follow-up, while 218 remained B1 inflammatory. We defined 518 genes that were differentially expressed in the ileum at diagnosis (FC≥1.5, FDR&lt;0.05) in B1 patients who later developed B2 stricturing complications vs. those who remained B1 throughout. These were notable for baseline up-regulation of OSM implicated in anti-TNF non-response, NCF2 and CSF3R implicated in myeloid cell activation, TGFBI implicated in tissue fibrosis, and a panel of 17 collagen genes in patients who progressed to stricturing. Sirius red staining confirmed an increase in sub-cryptal type I/III collagen in B1 patients at diagnosis who progressed to B2 behaviour. Of these 518 genes, we highlighted an inflammatory OSM co-expression signature that was tightly associated with an extracellular matrix COL1A2 co-expression signature (Pearson r = 0.88, p &lt; 0.0001). Network annotation analyses of those co-expression signatures showed that response to wounding, myeloid dendritic cells, and gp38+ stromal cells signatures are linked to both. Extracellular matrix (ECM) annotation, collagen binding, fibroblasts, and angiogenesis were more specific to the COL1A2 signature, and granulocytes and response to other organisms were more specific to the OSM co-expression signature. We further define small molecules targeting macrophage and fibroblast activation, and angiogenesis, which may reverse the stricturing gene signature including ephrin inhibitors, eicosatetraynoic acid (cyclooxygenase/lipoxygenase inhibitor), orantinib (PDGFR inhibitor), and PT-630 (fibroblast activation inhibitor). Our previous model containing serologies and a refined ECM gene set was significantly associated with stricturing development by year 5 (AUC:0.82)

Conclusion
An ileal gene program for macrophage and fibroblast activation is linked to future stricturing complications in treatment naïve paediatric CD, and may inform small-molecule therapeutic approaches.