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（由申请人提供）：抗生素耐药性是我们这个时代最关键的医学挑战之一。迫切需要理解抗生素作用的新范式来指导新的治疗策略。在马萨诸塞州总医院、麻省理工学院布罗德研究所和哈佛的导师指导下，这位候选人在耐药细菌病原体中发现了数十种对抗生素有反应的小非编码RNA分子（sRNA），这些分子以前并不知道参与对抗生素的转录反应。该提案旨在进一步研究这一有趣的发现，通过使用候选人已经通过RNA-Seq在关键ESKAPE病原体（肠球菌，金黄色葡萄球菌，克雷伯氏菌和E.大肠杆菌、不动杆菌属、假单胞菌属、肠杆菌属）。选择这些病原体进行研究是因为它们倾向于引起严重疾病并获得耐药性;它们被NIH，WHO，CDC和美国传染病协会认为是高度优先的威胁。将分析候选sRNA的序列保守性、与注释基因的表达共变以及预测的调控靶点。最高优先级的抗生素应答sRNA将被删除或过表达，这些干扰对抗生素应答的影响将通过抗生素活性、基础和诱导转录谱的测量以及鉴定结合伴侣和上位基因的测定来评估。初步 工作已经鉴定了一种sRNA，其缺失加速了寄生虫介导的杀伤。这些研究的结果将是了解这些sRNA在调节转录网络以响应抗生素暴露中的作用，目的是确定新的治疗靶点和策略。K 08指导临床科学家研究职业发展奖旨在培训候选人在四年内有效探索这一有前途的发现，为独立的研究生涯做准备。候选人的临床培训是在传染病，在分子生物学和生物化学博士培训之前。在这个职业发展奖的过程中，他将完成生物信息学方法的教学和实践培训，通过课程和实验来分析基因组规模的数据集，以及来自一个咨询委员会的培训，该委员会由在基因组方法，网络分析和细菌学方面具有集体专业知识的资深科学家组成。