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.

Public Health Relevance

Antibiotic resistance is one of the major biomedical challenges of our time. The investigators have found that a recently discovered class of molecules, small non-coding RNAs (sRNAs), are among the earliest transcripts to be regulated after antibiotic exposure in a variety of bacteria. This proposal seeks to identify and characteriz antibiotic-responsive sRNAs in important bacterial pathogens, and to study their function in order to investigate them as a new paradigm for understanding antibiotic resistance and devising new therapeutic strategies.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Clinical Investigator Award (CIA) (K08)
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Microbiology and Infectious Diseases B Subcommittee (MID)
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Huntley, Clayton C
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Massachusetts General Hospital
United States
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Gootenberg, Jonathan S; Abudayyeh, Omar O; Lee, Jeong Wook et al. (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438-442
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