Medically important flaviviruses, such as dengue (DENV) and West Nile (WNV) viruses, have displayed a tremendous ability to rapidly invade and coexist with other flaviviruses in new geographical areas. Vaccines and treatments for most of these viruses are lacking, warranting an urgent need for the development of inhibitors. Throughout this dissertation, I will describe our investigations into RNA-based therapeutics that were conducted with the goal of developing treatments for flavivirus infections. The work includes using intranasal administration as a portal of delivery for a small interfering RNA (siRNA) targeting the WNV envelope gene sequence as treatment for encephalitis caused by WNV. The data show that intranasal (i.n.) siRNA treatment can rescue mice from lethal WNV infection as late as 2-3 days prior to death. Importantly, i.n.-treated mice that survived primary WNV challenge were immune to a secondary WNV infection, indicating the potential of this approach in inducing protective immunity. Further, this work encompasses the design and characterization of a mismatched siRNA targeting the conserved 3' cyclization sequence (3'CS) that maps to the highly structured 3' untranslated region (3'UTR) of mosquito-borne flaviviruses, which is considered poorly accessible for binding by antisense molecules. The mismatched siRNA, msi3CS, demonstrates its potential for cross-inhibiting multiple flaviviruses including DENV-2, DENV-4 and WNV in cultured cells. Treatment of mice with msi3CS enabled protection against WNV encephalitis but was dependent on time of administration and host immune competence. Lastly, this work investigates the potential therapeutic use of an anti-apoptotic peptide during WNV infection for reducing neuropathology. These investigations reveal that the anti-apoptotic peptide surprisingly aids WNV-induced mortality indicating that reducing neuropathology alone may not be sufficient to improve prognosis.
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