Microbiome- and Host Inflammasome-Targeting Inhibitor Nanoliogmers are Therapeutic in Murine Colitis Model

Autoimmune and autoinflammatory diseases account for more than 80 chronic conditions affecting more than 24 million people in the US. Amongst these autoinflammatory diseases, non-infectious chronic inflammation of the gastrointestinal (GI) tract causes inflammatory bowel diseases (IBD), primarily Crohn’s and Ulcerative Colitis (UC). IBD is a complex disease, and one hypothesis is that these are either caused or worsened by compounds produced by bacteria in the gut. While traditional approaches have focused on pan immunosuppressive techniques (e.g., steroids), low remission rates, prolonged illnesses, and increased frequency of surgical procedures have prompted the search for more targeted and precision therapeutic approaches. IBD is a complex disease resulting from both genetic and environmental factors, but several recent studies have highlighted the potential pivotal contribution of gut microbiota dysbiosis. Gut microbiota are known to modulate the immune status of the gut by producing metabolites that are encoded in biosynthetic gene clusters (BGCs) of the bacterial genome. Here we show, a targeted and high-throughput screening of more than 90 biosynthetic genes in 41 gut anaerobes, through down selection using available bioinformatics tools, targeted gene manipulation in these genetically intractable organisms using Nanoligomer platform, and identification and synthesis of top microbiome-targets as a Nanoligomer BGC cocktail (SB_BGC_CK1, abbreviated as CK1) as a feasible precision therapeutics approach. Further, we used a host-directed immune-target screening to identify NF-κB and NLRP3 cocktail SB_NI_112 (or NI112 for short) as a targeted inflammasome inhibitor. We used these top two microbe- and host-targeted Nanoligomer cocktails in acute and chronic dextran sulfate sodium (DSS) mouse colitis and in TNFΔARE/+ transgenic mice that develop spontaneous Crohn’s like ilitis. The mouse microbiome was humanized to replicate that in human IBD through antibiotic treatment followed by mixed fecal gavage from 10 human donors and spiked with IBD-inducing microbial species. Following colonization, colitis was induced in mice using one week of 3% DSS (acute), or six weeks of 3 rounds of 2.5% DSS induction for a week followed by one week of no DSS (chronic colitis model). Both Nanoligomer cocktails (CK1 and NI112) showed a strong reduction in disease severity, significant improvement in disease histopathology, and profound downregulation of disease biomarkers in colon tissue as assessed by multiplexed ELISA. Further, we used two different formulations of intraperitoneal injections (IP) and Nanoligomer pills in the chronic DSS colitis model. Although both formulations were highly effective, the oral pill formulation demonstrated a greater reduction in biochemical markers compared to IP. A similar therapeutic effect was observed in the TNFΔARE/+ model. Overall, these results point to the potential for further development and testing of these inflammasome-targeting host-directed therapy (NI112), and more personalized microbiome-cocktails (CK1) for patients with recalcitrant IBD. TOC GRAPHIC