Bioinformatic and functional analysis of antibiotic-responsive small non-coding RNAs in bacterial pathogens

细菌病原体中抗生素反应性小非编码RNA的生物信息学和功能分析

• 批准号: 8949087
• 负责人: ROBY PAUL BHATTACHARYYA
• 金额: $ 18.21万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8949087
• 关键词: Acinetobacter; Advisory Committees; Americas; Antibiotic Resistance; Antibiotics; Antitoxins; Bacteria; Bacterial Genes; Bacteriology; Binding; Biochemistry; Bioinformatics; Biological Assay; Cell Wall; Centers for Disease Control and Prevention (U.S.); Clinical; Combined Antibiotics; Communicable Diseases; Computer Analysis; Data; Data Set; Disease; Drug resistance; Enterobacter; Enterococcus; Epistatic Gene; Escherichia coli; Exposure to; Gene Expression Profile; Gene Expression Regulation; General Hospitals; Genes; Genomics; Goals; Infection; Institutes; K-Series Research Career Programs; Klebsiella; Leadership; Massachusetts; Measures; Mediating; Mediator of activation protein; Medical; Mentors; Mentorship; Metabolism; Methodology; Methods; Molecular Biology; Nature; Outcome Study; Oxacillin; Pathway Analysis; Pharmaceutical Preparations; Physiological; Play; Positioning Attribute; Preparation; Production; Pseudomonas; Publications; RNA; Reading; Regulation; Regulatory Element; Regulatory Pathway; Research; Research Personnel; Resistance; Resolution; Role; Scientist; Senior Scientist; Sequence Analysis; Shapes; Societies; Staphylococcus aureus; Stress; Time; Toxin; Training; Transcript; United States National Institutes of Health; Untranslated RNA; Vancomycin; Virulence; Work; World Health Organization; career; combat; differential expression; drug development; experimental analysis; insight; killings; molecular phenotype; mutant; new therapeutic target; novel; novel diagnostics; novel therapeutics; overexpression; pathogen; programs; public health relevance; response; skills; small molecule; stressor; therapeutic target; transcriptome sequencing; transcriptomics; validation studies

 DESCRIPTION (provided by applicant): Antibiotic resistance is one of the most critical medical challenges of our time. New paradigms for understanding antibiotic action are desperately needed to direct new therapeutic strategies. Under the guidance of mentors at Massachusetts General Hospital and the Broad Institute of MIT and Harvard, the candidate has found dozens of antibiotic-responsive small non-coding RNA molecules (sRNAs) in drug- resistant bacterial pathogens that were not previously known to participate in the transcriptional response to antibiotics. This proposal seeks to further investigate this intriguing finding by systematically identifying antibiotic-responsive sRNAs using bioinformatic analysis of transcriptomic data that the candidate has already generated via RNA-Seq in the critical ESKAPE pathogens (Enterococcus, Staphylococcus aureus, Klebsiella and E. coli, Acinetobacter, Pseudomonas, Enterobacter). These pathogens were chosen for study because of their propensity to cause serious disease and to acquire drug resistance; they are recognized by the NIH, WHO, CDC, and Infectious Disease Society of America as high-priority threats. Candidate sRNAs will be analyzed for sequence conservation, covariation of expression with annotated genes, and predicted targets of regulation. The highest priority antibiotic-responsive sRNAs will be deleted or overexpressed, and the effects of these perturbations on the antibiotic response will be assessed through measures of antibiotic activity, basal and induced transcriptional profiling, and assays to identify binding partners and epistatic genes. Preliminary work has already identified one sRNA whose deletion accelerates antibiotic-mediated killing. The outcome of these studies will be to understand the role of these sRNAs in regulating transcriptional networks in response to antibiotic exposure, with the goal of identifying new therapeutic targets and strategies. This K08 Mentored Clinical Scientist Research Career Development Award proposal seeks to train the candidate to effectively explore this promising finding over a four-year period in preparation for an independent research career. The candidate's clinical training is in Infectious Disease, with prior doctoral training in molecular biology and biochemistry. During the course of this career development award, he will complete didactic and hands-on training in bioinformatic methodologies for analyzing genomic-scale datasets through coursework and experimentation, as well as training from an advisory committee of established senior scientists with collective expertise in genomic methodologies, network analysis, and bacteriology.

 描述（由适用提供）：抗生素耐药性是我们这个时代最关键的医学挑战之一。迫切需要采取新的治疗策略来理解抗生素作用的新范例。在马萨诸塞州综合医院的导师和麻省理工学院和哈佛大学研究所的指导下，该候选人发现，在药物耐药细菌病原体中，数十名抗生素反应性的小型非编码RNA分子（SRNA）以前尚不知道，这些病原体在对抗体剂的转录反应中没有参与。 This proposal seeks to further investigate this intriguing finding by systematically identifying antibiotic-responsive sRNAs using bioinformatic analysis of transcriptomic data that the candidate has already generated via RNA-Seq in the critical ESKAPE pathogens (Enterococcus, Staphylococcus aureus, Klebsiella and E. coli, Acinetobacter, Pseudomonas, Enterobacter).这些病原体被选择进行研究，因为它们承诺引起严重的疾病并获得耐药性。他们被NIH认可，NIH，美国疾病预防控制中心和美国传染病学会是高优先级威胁。将分析候选SRNA，以分析序列保守，与注释基因的表达协方差以及预测调节靶标。将通过抗生素活性，基本和诱导的转录分析和断言以鉴定结合伴侣和epistotic基因的措施来评估最高优先级抗生素反应性SRNA，这些扰动对抗生素反应的影响将得到评估。初步的 工作已经确定了一个SRNA，其缺失加速了抗生素介导的杀戮。这些研究的结果将是了解这些SRNA在响应抗生素暴露响应转录网络中的作用，目的是确定新的治疗靶标和策略。这项K08指导的临床科学家研究职业发展奖提案旨在培训候选人，以有效地探索四年期间的诺言发现，为独立研究职业做准备。候选人的临床培训是在传染病中进行的，并在分子生物学和生物化学方面进行了先前的博士培训。在这一职业发展奖的过程中，他将通过课程和实验完成生物信息学方法的教学和动手培训，用于分析的基因组规模数据集，以及拥有基因组方法，网络分析和细菌学集体专业知识的成熟高级科学家咨询委员会的培训。