Novel Nanoligomer-Based Therapeutics for Inflammatory Bowel Disease

项目总结-Sachi Bioworks开发了一个平台，可以快速生成Nanoligomers， 纳米颗粒结合的修饰的核酸寡聚体家族，其上调或下调 通过结合靶向DNA或mRNA选择蛋白质。在前期工作中，Sachi展示了 选择性靶向和改变免疫调节蛋白的表达， 厌氧菌，这表明纳米低聚物可以开发为炎症性肠病的潜在治疗方法。 疾病（IBD）或由肠道微生物群中的炎症过程促进的其他病症。这项I期 SBIR，Sachi建议应用该平台快速设计和构建针对生物合成基因的Nanoligomers 产生免疫调节代谢物的肠道微生物菌株中的BGC，然后测试这些 纳米寡聚体在体外和体内建立概念验证，以支持进一步开发， IBD的标准化或个性化治疗。目标1。设计和构建Nanoligomers以靶向BGC， 已知六种肠道细菌产生参与抗炎或炎症过程的代谢物 在肠道里。基于IBD和肠道微生物群的文献，Sachi确定了14种感兴趣的代谢物 在6种细菌的BGC中编码的蛋白（表3，研究策略）。为此，Sachi将利用该平台 a）设计和构建纳米寡聚体以靶向这些BGC中的每一种，B）进行体外测定以评估纳米寡聚体 以上调或下调相关细菌中靶代谢物的产生，以及c） 评估来自纳米寡聚体处理的细菌的裂解物对人外周血的免疫调节作用 单核细胞（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（每种代谢物三种）和2）从该组中选择两种纳米低聚物， PBMC细胞因子表达的最大变化（阈值：≤野生型促炎症表达的50% 细胞因子或抗炎细胞因子增加≥ 200%）。探索性：表征代谢物的变化 响应于纳米低聚物处理的生产。目标二。表征免疫调节和炎症 Nanoligomers在体内的作用。为了评估纳米低聚物对免疫调节和免疫抑制的作用， 炎症的标志物并在更复杂的活体动物肠环境中提供概念验证， Sachi将评估来自Aim 1的前两种Nanoligomers和一种错义Nanoligomers对肠道的影响 在慢性结肠炎和遗传性IBD小鼠模型中的微生物组和免疫应答。Sachi将评估 对结肠组织的组织学和结肠及血液中细胞因子产生的影响。辉煌与成功 标准：与对照组相比，抑制性纳米低聚物将使促炎细胞因子减少≥ 50%。 错义纳米寡聚体和活化纳米寡聚体将使抗炎细胞因子增加≥ 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 Nanoligomer处理的小鼠中的组织学结肠炎指数，以告知后续功效研究的设计。

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.