James McNamara, PhD

Associate Professor
Internal Medicine

Office: 3270C CBRB
Office Phone: 319-335-8491

Lab Website: https://mcnamara.lab.uiowa.edu/

RNA-based therapeutic approaches for nervous system disorders

The fluorophore is not fluorescent in the intact oligonucleotide due to its close proximity to the quencher. Upon digestion of the oligonucleotide, the quencher diffuses from the fluorophore which then exhibits fluorescence. The source of the target nuclease depends on the nature of the disease. For instance, in the case of infectious diseases, we are targeting nucleases produced by bacterial or viral pathogens; for cancer, we are targeting cancer-specific endogenous nucleases. Current projects include

1. development of a non-invasive imaging approach for focaStaphylococcusaureus (S. aureus) infections (see Hernandez et al., Nature Medicine, 2014); 2. creation of a rapid diagnostic assay fo S. aureus bacteremia (see Burghardt et al., PLoS One, 2016); 3. generation of a rapid diagnostic assay fo E. coliurinary tract infections (initial manuscript in preparation); 4. development of a rapid diagnostic assay for breast cancer via detection of circulating tumor cell- associated nucleases (initial manuscript in preparation). Among the more mature projects is an oligonucleotide-based approach for non-invasive imaging of bacterial infections. This approach exploits the ability of bacterial nucleases to degrade synthetic oligonucleotides that, due to particular chemical modifications, are resistant to degradation by mammalian serum nucleases (see Hernandez et al., Nature Medicine, 2014). Our recent results demonstrate that we can detect and localize focal S. aureusinfections in mice in less than 30 minutes with this approach. These results compare favorably with the current methods (biopsy and culture) which take at least a day to detect S. aureus in such infections. We have also developed methods for detecting bacteria in vitro in various clinical samples, such as blood and urine. This includes development of rapid assays for S. aureus bacteremia and E. coli urinary tract infections. S. aureus bacteremia is a substantial clinical problem with a high mortality rate. Current diagnostic methods require blood culturing methods that take more than a day to identify the causative pathogen. Our latest assay can rapidly identify S. aureus in blood without the need for culture (see Burghardt, et al., PLoS One, 2016). Similarly, current methods for reliably diagnosing urinary tract infections (the most common infection) require urine culturing methods that take more than a day. Our current assay for E. coli (the most common uropathogen) can detect this species in patient urine in under 3 hours. We anticipate that these approaches can address important unmet needs for infectious disease diagnostics. In the context of these ongoing projects, we are developing the basis for producing more advanced probes and more complex assays that we expect will greatly facilitate our ability to detect and identify target nucleases. For instance, we have identified the target nuclease of E. coli. In collaboration with Dr. Catherine Musselman, a structural biologist here, we have also generated diffactable crystals of a recombinant form of the protein and have developed a preliminary structural model. We anticipate that this structure may facilitate development of more specific assays for the nuclease. Finally, we have plans to develop multiplexed assays in which we use multiple probes with different-colored fluorophores to simultaneously detect multiple, distinct nucleases. Altogether, we expect these approaches will greatly enhance our ability to rapidly detect and identify a variety of disease-specific target nucleases, and to thereby provide the means of addressing a variety of unmet clinical diagnostic needs. tumor cell- associated nucleases (initial manuscript in preparation).

PubMed link

Department/Program Affiliations:
Internal Medicine
Molecular Medicine