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严峻的医学挑战之一，迫切需要在马萨诸塞州总医院和布罗德研究所的导师的指导下指导新的治疗策略。麻省理工学院和哈佛大学的候选人在耐药细菌病原体中发现了数十种抗生素反应性小非编码 RNA 分子（sRNA），这些分子以前并不知道它们参与抗生素的转录反应。通过对候选者通过 RNA-Seq 在关键 ESKAPE 病原体（肠球菌、金黄色葡萄球菌、克雷伯氏菌和大肠杆菌、不动杆菌、假单胞菌、肠杆菌）中已生成的转录组数据进行生物信息学分析，系统地识别抗生素反应性 sRNA，从而研究这一有趣的发现。选择这些病原体进行研究是因为它们容易引起严重疾病并获得耐药性；它们被 NIH、WHO、CDC 和美国传染病学会视为高度优先威胁，将分析候选 sRNA 的序列保守性、与注释基因的表达共变，并删除预测的响应性 sRNA。或过度表达，并且这些扰动对抗生素反应的影响将通过抗生素活性、基础和诱导转录分析以及鉴定结合伴侣的测定来评估和初步上位基因。 这项工作已经确定了一种 sRNA，其删除会加速抗生素介导的杀伤，这些研究的结果将是了解这些 sRNA 在响应抗生素暴露而调节转录网络中的作用，目的是确定新的治疗靶点和策略。 K08 指导临床科学家研究职业发展奖提案旨在培训候选人在四年内有效探索这一有希望的发现，为独立研究生涯做好准备。候选人的临床培训是传染病领域的，之前曾接受过传染病领域的博士培训。在获得该职业发展奖期间，他将通过课程作业和实验完成生物信息学方法学的教学和实践培训，以分析基因组规模的数据集，并接受由资深科学家组成的咨询委员会的培训。基因组方法学、网络分析和细菌学方面的集体专业知识。