Novel Nanoligomer-Based Therapeutics for Inflammatory Bowel Disease

项目摘要-Sachi Bioworks开发了一个快速生成纳米低聚物的平台，这是一种新型的 一类纳米颗粒结合的修饰核酸低聚物，可上调或下调 通过与目标DNA或信使核糖核酸结合来选择蛋白质。在前期工作中，萨奇展示了 选择性靶向并改变人肠道产生的免疫调节蛋白的表达 厌氧菌，这表明纳米低聚物可以作为一种潜在的治疗炎症性肠病的方法 疾病(IBD)或由肠道微生物区系中的炎症过程促进的其他情况。在此阶段I SBIR，Sachi建议应用这一平台来快速设计和构建针对生物合成基因的纳米低聚物 肠道微生物菌株中产生免疫调节代谢物的菌群(BGC)，然后测试这些 纳米低聚物在体外和体内建立概念验证以支持进一步的发展 IBD的标准化或个性化治疗。目标1.设计和制造靶向BGC的纳米低聚物 六种已知可产生参与抗炎或炎症过程的代谢物的肠道细菌 在肠子里。根据有关IBD和肠道微生物区系的文献，Sachi确定了14种感兴趣的代谢物 在6种细菌的BGC中编码(表3，研究策略)。在这个目标上，Sachi将使用这个平台 A)设计和构建针对每一种BGC的纳米寡聚体，b)进行体外试验以评估 每一种纳米低聚物在相关细菌中上调或下调目标代谢物的产生，以及c) 纳米低聚细菌裂解物对人外周血免疫调节作用的研究 单个核细胞(PBMC)。里程碑和成功标准：1)设计、构建和测试至少42 纳米低聚物(每个代谢物三个)和2)从该组中选择两个纳米低聚物产生 外周血单核细胞细胞因子表达变化最大(阈值：≤50%野生型促炎表达 细胞因子或≥在抗炎细胞因子中增加200%)。探索性：描述代谢物的变化 生产对纳米齐聚物处理的响应。目的2.免疫调节和炎症的特征 纳米低聚物在体内的作用。目的：评价纳米低聚物对免疫调节的影响。 炎症标志物，并在更复杂的活体动物肠道环境中提供概念证明， Sachi将评估来自Aim 1的前两个纳米低聚物和一个错义纳米低聚物对肠道的影响 慢性结肠炎和遗传性IBD小鼠模型中的微生物组和免疫反应。Sachi将评估 对结肠组织的组织学以及结肠和血液中细胞因子产生的影响。里程碑和成功 标准：抑制性纳米低聚物产生的促炎细胞因子≥比 错义纳米寡聚体和激活纳米寡聚体将产生≥抗炎细胞因子增加200% 与错义纳米低聚物相比。探索性：表征疾病活动指数和小鼠的变化 纳米低聚物治疗小鼠的组织学结肠炎指数，为后续疗效研究的设计提供信息。

PROJECT SUMMARY—Sachi Bioworks has developed a platform to rapidly generate Nanoligomers, a novel family of nanoparticle-bound, modified nucleic acid oligomers that up- or down-regulate the expression of selected proteins by binding to targeted DNA or mRNA. In preliminary work, Sachi demonstrated the ability to selectively target and alter the expression of immunomodulatory proteins produced by > 30 human gut anaerobes, which suggests Nanoligomers could be developed as a potential therapy for inflammatory bowel disease (IBD) or other conditions promoted by inflammatory processes in the gut microbiota. In this Phase I SBIR, Sachi proposes to apply this platform to rapidly design and build Nanoligomers to target Biosynthetic Gene Clusters (BGCs) in gut microbial strains that produce immunomodulatory metabolites and then test these Nanoligomers in vitro and in vivo to establish proof-of-concept to support further development as either a standardized or personalized treatment for IBD. Aim 1. Design and build Nanoligomers to target BGCs in six gut bacteria known to produce metabolites involved in anti-inflammatory or inflammatory processes in the intestine. Based on the literature on IBD and gut microbiota, Sachi identified 14 metabolites of interest encoded in BGCs in 6 species of bacteria (Table 3, Research Strategy). In this aim, Sachi will use the platform to a) design and build Nanoligomers to target each of these BGCs, b) conduct in vitro assays to assess the ability of each Nanoligomer to up- or down-regulate production of the target metabolite in the relevant bacteria, and c) assess the immunomodulatory effects of lysates from Nanoligomer-treated bacteria on human peripheral blood mononuclear cells (PBMCs). Milestones and Success Criteria: 1) Design, build, and test at least 42 Nanoligomers (three per metabolite) and 2) Select the two Nanoligomers from that group that produce the greatest change in PBMC cytokine expression (thresholds: ≤ 50% of wild-type expression of pro-inflammatory cytokines or ≥ 200% increase in anti-inflammatory cytokines). Exploratory: Characterize change in metabolite production in response to Nanoligomer treatment. Aim 2. Characterize immunomodulatory and inflammatory effects of the Nanoligomers in vivo. To assess the effects of the Nanoligomers on immunomodulation and markers of inflammation and provide proof-of concept in the more complex setting of a live animal intestine, Sachi will evaluate the effect of the top two Nanoligomers from Aim 1 and one missense Nanoligomer on the gut microbiome and immune responses in mouse models of chronic colitis and genetic IBD. Sachi will assess the effects on histology in colon tissue and cytokine production in the colon and blood. Milestones and Success Criteria: Inhibitory Nanoligomers will produce ≥ 50% decrease in pro-inflammatory cytokines compared to missense Nanoligomer and activating Nanoligomers will produce ≥ 200% increase in anti-inflammatory cytokines compared to missense Nanoligomer. Exploratory: Characterize change in the Disease Activity Index and Mouse Histology Colitis Index in Nanoligomer-treated mice to inform the design of subsequent efficacy studies.