Genetically Specific Therapy Against Pathogenic Bacteria

针对病原菌的基因特异性疗法

• 批准号: 8324190
• 负责人: C Jeffrey Brinker
• 金额: $ 38.1万
• 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/8324190
• 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）：随着细菌进化出对广谱抗生素的耐药性，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。环境问题是，我们大量使用抗生素，不分青红皂白地杀死细菌，正在破坏我们周围的微生物生态。我们需要一种新的策略，既能针对病原体，又不影响共生细菌或人类宿主，并且随着细菌的进化，这种策略将不断进化，以保持对感染性细菌的控制。我们的应用程序的广泛、长期目标是为这种新策略奠定基础。在这种方法中，细菌将被一种合成病毒或病毒样颗粒感染，这种病毒或病毒样颗粒将反义RNA带入细菌细胞，而不是杀死多种细菌的广谱抗生素。正如读者可能知道的，RNA在细胞中的几种用途之一是调节基因的表达。我们将模仿大自然，专门设计RNA来敲除致病细菌中的关键基因，而对有益细菌或人类宿主都没有影响。病毒样颗粒将携带几种不同的反义RNA，每一种反义RNA都足以杀死所针对的特定致病菌，或者使其失去毒性。细菌将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的设计是针对病原体的基因组的，它们可以随着病原体基因组的变化而重新设计，2)因为细菌将被多种致命RNA感染，因此不会有强大的选择压力，有利于细菌变体能够抵抗任何一种RNA的影响。当细菌对任何单一病原体产生耐药性都没有选择优势时，细菌对多种致命病原体产生耐药性的机会很小。我们的研究策略基于三个专业领域：1)生物信息学，从相关的基因组数据中提取所有可能敲除致病菌关键基因的反义RNA序列；2)纳米科学，诱导病毒样颗粒从组成蛋白质和核酸中自组装；3)微生物遗传学和生理学，以：a)将人类知识添加到计算机输出中，作为优先考虑潜在靶标的指南；b)对病原体进行实验，以评估反义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，其遗传和毒力机制已被广泛研究，这将对实验数据的解释有很大的优势。此外，沙门氏菌正在对几种抗生素产生耐药性。如果我们在实验室里成功对付沙门氏菌，我们的策略应该适用于各种各样的传染病。