Genetically Specific Therapy Against Pathogenic Bacteria

针对病原菌的基因特异性疗法

• 批准号: 8505508
• 负责人: C Jeffrey Brinker
• 金额: $ 36.77万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2015-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8505508
• 关键词: Address; Adverse effects; Affect; Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Antisense RNA; Area; Bacteria; Bacterial Genome; Bacterial Infections; Bioinformatics; Biomimetics; Cells; Code; Collaborations; Communicable Diseases; Computers; Containment; Data; Ecology; Engineering; Foundations; Gene Expression; Gene Proteins; Genes; Genetic; Genome; Genomics; Goals; Health; Hepatocyte; Human; Illinois; Knowledge; Laboratories; Malignant neoplasm of liver; Microbe; Microbial Genetics; Microbial Physiology; Microbiology; Molecular Biology; Mus; Nanotechnology; Nature; New Mexico; Nucleic Acids; Organism; Output; Peptides; Phage Display; Proteins; RNA; RNA Interference; RNA Sequences; Race; Reaction; Reader; Research; Resistance; Resistance development; Rest; Salmonella; Solutions; Specificity; Surface; Testing; Toxin; Variant; Virulence; Virulence Factors; Virus; Virus-like particle; Work; antimicrobial; arm; base; cancer cell; cancer therapy; cell type; commensal microbes; design; experience; genome-wide; immunogenic; immunogenicity; killings; knock-down; microbial; microbiome; nanoengineering; nanoscience; pathogen; pathogenic bacteria; pressure; research study; self assembly; skills

DESCRIPTION (provided by applicant): Humans are losing the arms race against infectious bacteria as bacteria evolve resistance to broad-spectrum antibiotics. This is both a health problem and an environmental problem. The health problem is that we are losing the ability to effectively treat many bacterial infections. The environmental problem is that we are disrupting the microbial ecology around us by intensive use of antibiotics that kill bacteria indiscriminately. We need a new strategy that will target pathogens without affecting either commensal bacteria or the human host, and that will evolve continually as bacteria evolve to maintain control over infectious bacteria. The broad, long term objective of our application is to lay the foundations for such a new strategy. In this approach, instead of a broad spectrum antibiotic that kills many types of bacteria the bacteria would be infected by a synthetic virus, or virus-like particle, that brings into the bacterial cells antisense RNA. As the reader probably knows, one of the several uses of RNA in the cell is to regulate the expression of genes. We will emulate nature by designing RNA specifically to knock down critical genes in pathogenic bacteria only, and to have no effect on either beneficial bacteria or the human host. The virus-like particles will carry several different antisense RNA's, each of which separately will be sufficient to either kill or render nonvirulent the particular pathogenic bacterium that is being targeted. Bacteria will find it very difficult to evolve resistance to this approach for two fundamental reasons: 1) Because the antisense RNA's are designed to be specific to the pathogen's genome, they can be redesigned as the pathogen's genome changes, and 2) because the bacteria will be infected with multiple lethal RNA, there will not be a strong selection pressure favoring bacterial variants that can resist the effects of any one of the RNA's. The chances of a bacterium developing resistance to multiple lethal agents, when there is no selection advantage for developing resistance to any single agent, is small. Our research strategy rests on three areas of expertise: 1) bioinformatics to extract from the relevant genomic data all the antisense RNA sequences that could potentially knock down critical genes in the pathogenic bacteria, 2) nanoscience to induce the self-assembly of the virus-like particles from the constituent proteins and nucleic acids, and 3) microbial genetics and physiology to: a) add human knowledge to the computer outputs as a guide to prioritizing potential targets and b) to do the experiments on the pathogens in order to assess the effects of the antisense RNA. These three areas of expertise are embodied in the collaborating laboratories of Eric Jakobsson (bioinformatics), Jeff Brinker (nanoscience) and Stanley Maloy (microbiology). For this initial project we have chosen Salmonella as the target. Salmonella is an important pathogen whose genetics and mechanisms of virulence have been extensively studied, which will be a big advantage in interpreting experimental data. Also, Salmonella is acquiring resistance to several antibiotics. If we succeed in the laboratory with Salmonella, our strategy should be applicable to a wide variety of infectious diseases.

描述（由申请人提供）：随着细菌对广谱抗生素产生耐药性，人类正在输掉与传染性细菌的军备竞赛。这既是一个健康问题，也是一个环境问题。健康问题是我们正在失去有效治疗许多细菌感染的能力。环境问题在于，我们大量使用不加区别地杀死细菌的抗生素，破坏了我们周围的微生物生态。我们需要一种新的策略，能够在不影响共生细菌或人类宿主的情况下针对病原体，并且随着细菌的进化而不断进化，以保持对传染性细菌的控制。我们应用的广泛、长期目标是为这样的新战略奠定基础。在这种方法中，细菌将被合成病毒或病毒样颗粒感染，而不是杀死多种细菌的广谱抗生素，这些颗粒将反义RNA带入细菌细胞。读者可能知道，RNA 在细胞中的多种用途之一是调节基因的表达。我们将效仿自然，专门设计RNA，仅敲除病原细菌中的关键基因，而不对有益细菌或人类宿主产生影响。病毒样颗粒将携带几种不同的反义RNA，每种反义RNA都足以杀死所针对的特定病原细菌或使其无毒力。细菌会发现很难进化出对这种方法的抗性，原因有两个：1) 因为反义 RNA 被设计为针对病原体基因组，它们可以随着病原体基因组的变化而重新设计，2) 因为细菌会当细菌被多种致命RNA感染时，不会有强大的选择压力有利于能够抵抗任何一种RNA影响的细菌变体。当细菌对多种致死剂产生抗药性时，如果没有选择优势对任何单一药物产生抗药性，那么细菌对多种致死剂产生抗药性的机会很小。我们的研究策略基于三个专业领域：1) 生物信息学，从相关基因组数据中提取所有反义 RNA 序列，这些序列可能会敲除致病细菌中的关键基因；2) 纳米科学，诱导病毒自组装 -例如来自组成蛋白质和核酸的颗粒，以及 3) 微生物遗传学和生理学：a) 将人类知识添加到计算机输出中，作为优先考虑潜在目标的指南；b) 对病原体进行实验，以便评估反义RNA的作用。这三个专业领域体现在 Eric Jakobsson（生物信息学）、Jeff Brinker（纳米科学）和 Stanley Maloy（微生物学）的合作实验室中。对于这个初始项目，我们选择沙门氏菌作为目标。沙门氏菌是一种重要的病原体，其遗传学和毒力机制已被广泛研究，这将在解释实验数据方面具有很大优势。此外，沙门氏菌正在对几种抗生素产生耐药性。如果我们在沙门氏菌实验室取得成功，我们的策略应该适用于多种传染病。