Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease

Abstract

Objective: Inflammatory bowel diseases cause significant morbidity and mortality. Aberrant NF-κB signalling is strongly associated with these conditions, and several established drugs influence the NF-κB signalling network to exert their effect. This study aimed to identify drugs which alter NF-κB signalling and may be repositioned for use in inflammatory bowel disease.Design: The SysmedIBD consortium established a novel drug-repurposing pipeline based on a combination of in-silico drug discovery and biological assays targeted at demonstrating an impact on NF-kappaB signalling, and a murine model of IBD.Results: The drug discovery algorithm identified several drugs already established in IBD, including corticosteroids. The highest-ranked drug was the macrolide antibiotic Clarithromycin, which has previously been reported to have anti-inflammatory effects in aseptic conditions.Clarithromycin's effects were validated in several experiments: it influenced NF-κB mediated transcription in murine peritoneal macrophages and intestinal enteroids; it suppressed NF-κB protein shuttling in murine reporter enteroids; it suppressed NF-κB (p65) DNA binding in the small intestine of mice exposed to LPS, and it reduced the severity of dextran sulphate sodium-induced colitis in C57BL/6 mice. Clarithromycin also suppressed NF-κB (p65) nuclear translocation in human intestinal enteroids.Conclusions: These findings demonstrate that in-silico drug repositioning algorithms can viably be allied to laboratory validation assays in the context of inflammatory bowel disease; and that further clinical assessment of clarithromycin in the management of inflammatory bowel disease is required.

Effects of Human RelA Transgene on Murine Macrophage Inflammatory Responses

“…In our own earlier studies using the p65-DsRedxp/IκBα-eGFP double transgenic strain, we successfully showed that TNF induced p65 oscillations in murine intestinal-stem cell derived 3D organoid cultures [21]. In those experiments, we observed a first, synchronised wave of p65 nuclear translocation, followed by a second wave of partially synchronised translocation [21]. In the current study, we observed one wave of nuclear translocation in p65-DsRedxp/IκBα-eGFP macrophages upon LPS stimulation.…”

“…The p65-DsRedxp reporter mouse has previously been used for live fluorescence imaging of mouse intervertebral disc (IVD) explants, where it was shown that the RelA(p65) subunit translocated to nucleus of cells within the IVD following stimulation with IL-1β or TNF [20]. In our own earlier studies using the p65-DsRedxp/IκBα-eGFP double transgenic strain, we successfully showed that TNF induced p65 oscillations in murine intestinal-stem cell derived 3D organoid cultures [21]. In those experiments, we observed a first, synchronised wave of p65 nuclear translocation, followed by a second wave of partially synchronised translocation [21].…”

“…Recently, a novel transgenic mouse expressing human p65 tagged with Discosoma red fluorescent protein (DsRedxp) was reported, with confocal microscopy used to monitor human RelA(p65) during the circadian cycle in murine intervertebral disc explant cultures [20], and in cytokine activated bone marrow-derived macrophages (BMDMs) [10]. We also utilised this same strain to generate murine intestinal crypt stem-cell derived 3D organoid cultures expressing p65-DsRedxp, to study the effect of the macrolide antibiotic clarithromycin on p65 nucleocytoplasmic shuttling [21]. To understand further cell-specific pathways in this mouse, we have examined the functional implication of xenogeneic (human) RelA protein on murine macrophage biology, investigating the transcriptional responses to inflammatory stimuli.…”

BioUML—towards a universal research platform

“…It takes data in multiple formats and automatically generates hypotheses about molecular mechanisms of studied pathologies, finds most promising drug targets and biomarkers and suggests drugs and active compounds as treatment candidates for the pathology. With the help of Genome Enhancer, several successful studies were performed including: identification of early diagnostic biomarkers of colorectal cancer ( 31 ); study of potential mechanisms of atherosclerosis ( 32 ); drug repurposing in IBD ( 33 ).…”

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

“…This creates an imbalance in such databases towards human studies. Nevertheless, due to the lack of species specific pathway databases and especially due to the lack of experimental data to establish such databases, previous studies also used similar pathway databases to perform an upstream analysis in different animal species [129,210,211,[271][272][273]. However, the reduced applicability of such pathway databases to animal species increases the need to experimentally validate the findings proposed in my studies.…”