RNA Therapeutics for Infectious Diseases: Viral Hemorrhagic Fever

Background: Viral hemorrhagic fever (VHF) is caused by several distinct families of RNA viruses (flaviviruses, arenaviruses, hantaviruses, and filoviruses). Because these viruses have RNA genomes that are replicated by error-prone polymerases, they can undergo frequent mutations and possess a unique ability to adapt to changing environments and cause emerging diseases in humans. Such viruses can cause severe disease associated with high mortality and are a significant threat to our deployed Warfighters. Although these viruses are generally restricted to certain geographical areas, they can spread to humans and be transmitted from person to person. VHF outbreaks are difficult to prevent since they can occur sporadically and are challenging to forecast. The few available vaccines and therapeutics have limited efficacy and are not Food and Drug Administration (FDA)-approved. In the absence of a unified global response to a pandemic virus, the development of new monoclonal antibodies or vaccines can take years, and most pharmaceutical companies lack the economic incentive to prioritize these pathogens in developing nations. Objective/Hypothesis: To address the global burden of VHF and its impact on our military forces, we propose to expand our RNA-based therapeutics platform to develop effective medical countermeasures for VHF for preventive or therapeutic use. Our flexible platform of small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) can accommodate for these continuously evolving viruses and will be rapidly available for future outbreaks. To provide broad coverage against hantavirus and arenavirus family members, we will target highly conserved regions of the viral genome, host proteins that are broadly required for viral propagation, or a combination of such targets. Our team at the University of Massachusetts Chan Medical School (UMass Chan) has a robust oligonucleotide (oligo) drug-based therapeutics research strategy directed against many human diseases. For example, our oligo drugs are revolutionizing the treatment of liver disease with a single administration supporting multi-month clinical efficacy with an excellent safety profile. We have also successfully engineered small RNA-based effectors against SARS-CoV-2 with proven efficacy in vitro and in vivo. Our proposal will produce at least one candidate for pre-IND studies. Rationale: Oligo drugs have revolutionized human medicine-several are FDA-approved for liver indications- and additional agents are on the horizon. Our oligo drug development platform is transformative for the following reasons: (1) unprecedented duration of effect (up to 6 months following a single injection), (2) clean safety profile, (3) high specificity, and (4) functionality based on genome sequence information. Oligo drugs are ideal as a quick acting treatment following virus exposure, provided safe and efficient delivery is achieved. The mechanism of action relies on rapid (within 12 hours) and persistent activation of the innate immune system. Once the sequence of a virus is known, advanced mapping tools can be used to design a virus-specific therapeutic within 48 hours. Manufacturers can scale up oligo drug production to treat millions of people within months of identifying new threats. Specific Aims: Aim 1. Identify top host factors required for virus propagation (using proteomics- and CRISPR-based screening approaches), and determine their mechanisms of action in relevant cell models. Identify virus genome sequences to target. Aim 2. Design and develop custom oligo drugs with high efficacy and targeting specificity in relevant cell lines and tissues. Aim 3. Optimize oligo-based therapeutics against VHF in animal models. Study Design: We will design and synthesize oligo drugs targeting maximally conserved regions of the representative arena- and hantaviruses, fine-tuning our well-established pipeline. Our oligo drugs will feature a chemical scaffold that supports functional, sustained delivery to the lung, immune cells, and/or the liver. We will screen 10-20 small RNAs for each viral gene and identify fully modified hyper-functional in vivo active compounds that decrease the viral load. To mitigate for viral escape mutations, we will screen multitargeting constructs for multiple viral genes or genome elements. We will target known host factors required for VHF as well as new targets that we identify. The top viral and host gene-targeting siRNAs/ASOs will be combined in a single multitargeting construct that minimizes viral infection/replication and dampens excessive inflammatory responses. We can develop formulations with broad-spectrum activity against all VHFs. We will assess outcomes in animal models, such as weight loss and survival, viral load, and inflammation/necrosis in vital organs, comparing different delivery methods. Relevance: VHFs are a significant threat to our service members but have been relatively understudied by the scientific community. This lack of knowledge has created a significant gap in our ability to treat and prevent these infections. There is also precedence for VHFs as biological weapons. Oligo drugs are ideal for combating VHF because a single dose can provide long-lasting protection, are well-suited for both prevention and treatment strategies, can be rapidly produced at a low cost, are stable at tropical temperatures where many of these infections occur, and do not require a cold chain. Once our platform is optimized to combat VHF, we can easily apply our strategy to target other viral pathogens of interest. Less