Background In Inflammatory Bowel Disease (IBD), intestinal barrier dysfunction and epithelial cell injury are believed to be associated with activation of the immune system to drive disease-associated inflammation, which together constitute key features of active disease. Existing drugs used to treat IBD induce endoscopic remission and improvements in mucosal healing in only a minor proportion of patients, driving a critical need for therapies which lead directly to mucosal healing. Furthermore, predicting patients who may benefit from therapeutics that address specific mechanisms of mucosal healing may augment response rates. Methods We screened proteins, identified from a meta-analysis of healthy human microbiome, in cellular assays and animal models related to mucosal injury, with the goal of identifying novel therapeutics that have the potential to directly induce mucosal healing. The proteins identified were further optimized by protein engineering to increase their stability as well as gastro-intestinal (GI) targeting via oral administration. For this, therapeutic proteins were expressed using a probiotic, Lactococcus lactis (L.lactis), engineered to display the recombinant proteins on the cell surface, and evaluated for activity in DSS- and DNBS-induced models of colitis in mice. Mechanism of action studies using computational and laboratory based methods to analyze gene expression and direct molecular interactions with human proteins, enabled the identification of pathways modulated by the candidate molecules. These pathways were further evaluated for their ability to identify biomarkers in specific patients most suitable for treatment in a precision medicine approach. Results We have identified a novel, healthy microbiome-derived protein that demonstrated robust activity in human epithelial injury assays in vitro. The protein reduced intestinal injury related pathology in mice when orally administered to target directly the GI tract. SG-5-00455, the product based on an L.lactis strain expressing the candidate therapeutic protein, reduced pathology scores, inflammation and barrier function related LPS-binding protein levels to levels comparable to those obtained glucagon-like peptide 2 (GLP-2), as well as improving dysregulated tissue repair and fibrosis-associated gene expression and proteins levels. SG-5-0455 treatment did not result in systemic exposure, driving its therapeutic activity in a GI-localized manner by targeting pathways related to tissue injury and fibrinolysis. Conclusion SG-5-00455, through its novel mechanism of action and oral delivery to directly target tissue repair pathways in the GI-tract, offers the potential to address a large critical need in IBD.

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Intestinal barrier dysfunction or the loss of the epithelial integrity allowing the permeation of microorganisms, dietary antigens and other particles into the gastrointestinal (GI) mucosa results in the activation of the immune system and drives inflammation during IBD. Ongoing inflammation in the GI tract and loss of the mucosal barrier are key features of active disease and predict relapse and serious complications. Existing drugs approved in IBD have limited effects on endoscopic remission and improvement in mucosal healing, driving a critical need for therapies which lead directly to mucosal healing. We have identified a microbial protein, SG-2-0776, that directly improves barrier function and reduces fibrogenesis in vitro and in vivo with potential to become a driver of mucosal healing. SG-2-0776 was identified through a novel algorithm, multi-technology meta-analysis (MTMA), using mucosal biopsies from UC patients and control subjects. Two bacterial strains, Eubacterium eligens and Roseburia hominis were significantly reduced in UC samples. Screening of proteins predicted to be secreted from these strains using in vitro transepithelial/endothelial electrical resistance (TEER) and wound healing assays, identified SG-2-0776, a novel protein, which significantly improved epithelial barrier integrity and reduced fibrogenesis. Administration of recombinant SG-2-0776 protein showed improvement in intestinal barrier function, reduced inflammation and fibrosis in rodent models of colitis. Moreover, SG-2-0776 was expressed in Lactococcus lactis as a delivery vehicle and administered orally to act locally for therapeutic effects in these models of colitis. Mechanism of action studies demonstrated that SG-2-0776 interacts with extracellular matrix proteins regulating myofibroblasts differentiation, leading to reduced fibrogenic phenotypes. Altogether, these results demonstrate SG-2-0776 has the potential, as a standalone or adjunct therapy to existing treatments, to ameliorate mucosal barrier function and prevent fibrogenesis in IBD patients.